Mon Mar 21 17:56:06 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 /usr/local/freesurfer/stable5/bin/recon-all -all -s good_output_5.1 subjid good_output_5.1 setenv SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110321 Linux compute-0-1.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse 4194304 kbytes vmemoryuse 8388608 kbytes descriptors 4096 memorylocked 4194304 kbytes maxproc 268288 total used free shared buffers cached Mem: 32962780 2192904 30769876 0 59436 221500 -/+ buffers/cache: 1911968 31050812 Swap: 32764556 1973480 30791076 ######################################## program versions used $Id: recon-all,v 1.379 2011/03/16 16:20:27 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:08-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_convert.c,v 1.179 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:09-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: tkregister2.c,v 1.121 2011/03/01 01:41:22 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:11-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:11-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:11-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:11-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:11-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:11-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:12-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:12-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:12-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:13-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:13-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:14-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:15-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:15-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:16-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:17-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:17-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:18-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:18-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:19-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:19-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:23-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:24-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:25-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:27-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:30-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:30-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:31-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:31-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:32-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mris_calc.c,v 1.37 2011/03/11 21:13:13 rudolph Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:33-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:34-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:34-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:34-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:34-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/03/21-21:56:35-GMT BuildTimeStamp: Mar 21 2011 05:48:55 CVS: $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/stable5/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Mar 21 17:56:38 EDT 2011 Found 4 runs /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_robust_template --mov /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006.mgz --average 1 --template /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003-iscale.txt /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004-iscale.txt /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005-iscale.txt /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006-iscale.txt --subsample 200 --lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz as movable/source volume. --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004.mgz as movable/source volume. --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005.mgz as movable/source volume. --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006.mgz as movable/source volume. Total: 4 input volumes --average: Using method 1 for template computation. --template: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz'... reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004.mgz'... reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005.mgz'... reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/004.mgz ) to TP 1 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0510677 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.134992 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.289835 ), max sat: 8 ( 0.134992 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 6 ( 0.198691 ), max sat: 8 ( 0.134992 ), sat diff: 2 -- Iteration: 5 trying sat: 7 min sat: 6 ( 0.198691 ), max sat: 7 ( 0.161416 ), sat diff: 1 -- Iteration: 6 trying sat: 6.5 - final SAT: 7 ( it: 6 , weight check 0.161416 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.2343023547553 0 1.0000000000000 0 1.9495317750505 0 0 1.0000000000000 -1.0355476336448 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 0.294883 Iteration(f): 2 -- diff. to prev. transform: 0.240949 Iteration(f): 3 -- diff. to prev. transform: 0.201137 Iteration(f): 4 -- diff. to prev. transform: 0.255175 Iteration(f): 5 -- diff. to prev. transform: 0.273283 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 0.62108 Iteration(f): 2 -- diff. to prev. transform: 0.12048 Iteration(f): 3 -- diff. to prev. transform: 0.0154686 Iteration(f): 4 -- diff. to prev. transform: 0.0284834 Iteration(f): 5 -- diff. to prev. transform: 0.0205718 max it: 5 reached! Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.25473 Iteration(f): 2 -- diff. to prev. transform: 0.0415062 Iteration(f): 3 -- diff. to prev. transform: 0.0060009 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.037654 Iteration(f): 2 -- diff. to prev. transform: 0.00305546 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.0572993 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00233612 < 0.01 :-) - final transform: Tf = [ ... 0.9999952532724 0.0030807619812 -0.0000483559178 -0.3593856351262 -0.0030808431754 0.9999936700650 -0.0017799537137 0.8939839744116 0.0000428719980 0.0017800942417 0.9999984147120 -0.1344765713439 0 0 0 1.0000000000000 ] - final iscale: If = 1.00741 [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/005.mgz ) to TP 1 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0459896 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.121093 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.270528 ), max sat: 8 ( 0.121093 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 4 ( 0.270528 ), max sat: 6 ( 0.171163 ), sat diff: 2 -- Iteration: 5 trying sat: 5 min sat: 5 ( 0.212132 ), max sat: 6 ( 0.171163 ), sat diff: 1 -- Iteration: 6 trying sat: 5.5 - final SAT: 6 ( it: 6 , weight check 0.171163 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 0.0806232774706 0 1.0000000000000 0 -0.8587878652708 0 0 1.0000000000000 0.2893228397368 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 0.693533 Iteration(f): 2 -- diff. to prev. transform: 0.356665 Iteration(f): 3 -- diff. to prev. transform: 0.221343 Iteration(f): 4 -- diff. to prev. transform: 0.0790383 Iteration(f): 5 -- diff. to prev. transform: 0.0497159 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 0.627751 Iteration(f): 2 -- diff. to prev. transform: 0.071911 Iteration(f): 3 -- diff. to prev. transform: 0.0207046 Iteration(f): 4 -- diff. to prev. transform: 0.0224564 Iteration(f): 5 -- diff. to prev. transform: 0.00352928 < 0.01 :-) Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.0924509 Iteration(f): 2 -- diff. to prev. transform: 0.0040507 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.0510274 Iteration(f): 2 -- diff. to prev. transform: 0.00223367 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.0745268 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00101638 < 0.01 :-) - final transform: Tf = [ ... 0.9999802186722 0.0062650551716 -0.0005579857407 -0.6093224297684 -0.0062675520081 0.9999698178567 -0.0045914232603 1.5307222443389 0.0005292033795 0.0045948296405 0.9999893036850 -0.4733785840426 0 0 0 1.0000000000000 ] - final iscale: If = 0.995414 [init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/006.mgz ) to TP 1 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig/003.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0440043 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.11956 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.266169 ), max sat: 8 ( 0.11956 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 4 ( 0.266169 ), max sat: 6 ( 0.169667 ), sat diff: 2 -- Iteration: 5 trying sat: 5 min sat: 5 ( 0.209271 ), max sat: 6 ( 0.169667 ), sat diff: 1 -- Iteration: 6 trying sat: 5.5 - final SAT: 6 ( it: 6 , weight check 0.169667 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 0.3738766040319 0 1.0000000000000 0 -1.0419889793102 0 0 1.0000000000000 -0.1815358958855 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 0.870795 Iteration(f): 2 -- diff. to prev. transform: 0.475828 Iteration(f): 3 -- diff. to prev. transform: 0.702409 Iteration(f): 4 -- diff. to prev. transform: 0.460156 Iteration(f): 5 -- diff. to prev. transform: 0.254227 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 0.583628 Iteration(f): 2 -- diff. to prev. transform: 0.0611544 Iteration(f): 3 -- diff. to prev. transform: 0.0218413 Iteration(f): 4 -- diff. to prev. transform: 0.00882035 < 0.01 :-) Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.0665332 Iteration(f): 2 -- diff. to prev. transform: 0.00941424 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.167613 Iteration(f): 2 -- diff. to prev. transform: 0.00753165 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.131601 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00326723 < 0.01 :-) - final transform: Tf = [ ... 0.9999916172533 0.0040559314020 -0.0005611092504 -0.2904089323400 -0.0040567874893 0.9999905960353 -0.0015330740971 1.1135515952652 0.0005548859304 0.0015353375467 0.9999986674192 -0.0809349067904 0 0 0 1.0000000000000 ] - final iscale: If = 0.993285 warping movs and creating initial template... allow intensity scaling using median Writing final template: /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/rawavg.mgz Writing final transforms (warps etc.)... registration took 2 minutes and 8 seconds. /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/rawavg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig.mgz --conform mri_convert /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/rawavg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179 2011/03/16 21:23:48 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Mar 21 17:59:01 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Mar 21 18:00:15 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7938, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable5/bin/extract_talairach_avi_QA.awk /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach_avi.log TalAviQA: 0.97980 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Mar 21 18:00:18 EDT 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri /usr/local/freesurfer/stable5/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux compute-0-1.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux Mon Mar 21 18:00:21 EDT 2011 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.23859 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23859/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23859/nu0.mnc -odt float input_transform: error reading transform. error loading transform from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179 2011/03/16 21:23:48 nicks Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.23859/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Mar 21 18:00:30 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.23859/nu0.mnc ./tmp.mri_nu_correct.mni.23859/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23859/0/ [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:00:33] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23859/0/ ./tmp.mri_nu_correct.mni.23859/nu0.mnc ./tmp.mri_nu_correct.mni.23859/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 28 CV of field change: 0.000996719 [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:02:09] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23859/nu0.mnc ./tmp.mri_nu_correct.mni.23859/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Mar 21 18:02:27 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.23859/nu1.mnc ./tmp.mri_nu_correct.mni.23859/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23859/1/ [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:02:31] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23859/1/ ./tmp.mri_nu_correct.mni.23859/nu1.mnc ./tmp.mri_nu_correct.mni.23859/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000983558 [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:04:04] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23859/nu1.mnc ./tmp.mri_nu_correct.mni.23859/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23859/ones.mgz $Id: mri_binarize.c,v 1.26 2011/03/02 00:04:13 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23859/ones.mgz sysname Linux hostname compute-0-1.local machine x86_64 user khoa input ./tmp.mri_nu_correct.mni.23859/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.23859/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/input.mean.dat $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/input.mean.dat sysname Linux hostname compute-0-1.local machine x86_64 user khoa Loading ./tmp.mri_nu_correct.mni.23859/ones.mgz Loading orig.mgz input_transform: error reading transform. error loading transform from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23859/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/output.mean.dat $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/output.mean.dat sysname Linux hostname compute-0-1.local machine x86_64 user khoa Loading ./tmp.mri_nu_correct.mni.23859/ones.mgz Loading ./tmp.mri_nu_correct.mni.23859/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23859/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.23859/nu2.mnc ./tmp.mri_nu_correct.mni.23859/nu2.mnc mul 1.05068900363734836688 Saving result to './tmp.mri_nu_correct.mni.23859/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.23859/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.23859/nu2.mnc nu.mgz --like orig.mgz input_transform: error reading transform. error loading transform from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179 2011/03/16 21:23:48 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.23859/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 10 seconds. mapping (13, 126) to ( 3, 110) Mon Mar 21 18:05:47 EDT 2011 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Mon Mar 21 18:05:48 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 10 seconds. MRIsplineNormalize(): npeaks = 17 Starting OpenSpline(): npoints = 17 white matter peak found at 111 white matter peak found at 108 gm peak at 56 (56), valley at 33 (33) csf peak at 10, setting threshold to 40 white matter peak found at 111 white matter peak found at 110 gm peak at 59 (59), valley at 34 (34) csf peak at 10, setting threshold to 42 #-------------------------------------------- #@# Skull Stripping Mon Mar 21 18:08:00 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable5/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (50, 30, 19) --> (205, 238, 223) using (102, 99, 121) as brain centroid... mean wm in atlas = 126, using box (83,73,96) --> (121, 124,146) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 initial log_p = -10407.5 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.3, 4.8, -9.4): log p = -10319.262 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10318.4, old_max_log_p =-10319.3 (thresh=-10308.9) 1.075 0.000 0.000 -9.737; 0.000 1.075 0.000 -3.892; 0.000 0.000 1.000 -9.375; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10298.3, old_max_log_p =-10318.4 (thresh=-10308.0) 1.094 -0.002 0.033 -17.711; 0.000 1.134 0.067 -14.917; -0.037 -0.071 1.035 -2.586; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10279.2, old_max_log_p =-10298.3 (thresh=-10288.0) 1.114 0.034 -0.001 -20.243; -0.034 1.200 0.034 -12.156; -0.002 -0.034 1.018 -9.204; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10273.5, old_max_log_p =-10279.2 (thresh=-10268.9) 1.093 -0.005 -0.002 -13.150; 0.002 1.223 0.034 -19.448; -0.002 -0.034 1.018 -9.204; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10268.7, old_max_log_p =-10273.5 (thresh=-10263.2) 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 10268.7 tol 0.000010 Resulting transform: 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10268.7 (old=-10407.5) transform before final EM align: 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1144141.8 tol 0.000000 final transform: 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 21 minutes and 49 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=103 z=121 r=81 first estimation of the main basin volume: 2306073 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=109, y=86, z=84, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=15566830697 voxels, voxel volume =1.000 = 15566830697 mmm3 = 15566830.592 cm3 done. PostAnalyze...Basin Prior 120 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=109, z=114, r=10061 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=39 , nb = 44712 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=25 , nb = 2790 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=18 , nb = 2610 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 19674 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=41 , nb = 19188 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=45 , nb = 450 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 31, 24, 58 after analyzing : 25, 31, 31, 37 RIGHT_CER before analyzing : 25, 30, 38, 70 after analyzing : 25, 35, 38, 43 LEFT_CER before analyzing : 18, 19, 25, 68 after analyzing : 18, 23, 25, 34 RIGHT_BRAIN before analyzing : 38, 31, 23, 58 after analyzing : 25, 31, 31, 37 LEFT_BRAIN before analyzing : 41, 33, 25, 58 after analyzing : 26, 33, 33, 39 OTHER before analyzing : 45, 80, 88, 95 after analyzing : 45, 85, 88, 87 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 68.656, std = 8.184 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.76, sigma = 3.93 after rotation: sse = 2.76, sigma = 3.93 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.82, its var is 3.45 before Erosion-Dilatation 0.15% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...37 iterations mri_strip_skull: done peeling brain Brain Size = 1541767 voxels, voxel volume = 1.000 mm3 = 1541767 mmm3 = 1541.767 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Mar 21 18:30:27 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (62, 49, 38) --> (194, 160, 203) using (106, 86, 121) as brain centroid... mean wm in atlas = 107, using box (90,72,101) --> (122, 99,141) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -7447.8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, 8.5, -8.5): log p = -7134.978 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6993.7, old_max_log_p =-7135.0 (thresh=-7127.8) 1.064 0.000 0.000 -8.688; 0.000 1.226 0.140 -32.353; 0.000 -0.150 0.991 9.014; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6993.7, old_max_log_p =-6993.7 (thresh=-6986.7) 1.064 0.000 0.000 -8.688; 0.000 1.226 0.140 -32.353; 0.000 -0.150 0.991 9.014; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6883.4, old_max_log_p =-6993.7 (thresh=-6986.7) 1.064 0.000 0.000 -10.563; 0.000 1.256 0.077 -28.441; 0.000 -0.068 0.980 -2.362; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6877.7, old_max_log_p =-6883.4 (thresh=-6876.5) 1.064 0.000 0.000 -10.563; 0.000 1.253 0.109 -30.011; 0.000 -0.111 0.995 2.463; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6842.9, old_max_log_p =-6877.7 (thresh=-6870.8) 1.065 -0.020 -0.010 -7.404; 0.017 1.252 0.092 -30.654; 0.009 -0.091 0.994 -0.867; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6842.9, old_max_log_p =-6842.9 (thresh=-6836.0) 1.065 -0.020 -0.010 -7.404; 0.017 1.252 0.092 -30.654; 0.009 -0.091 0.994 -0.867; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06481 -0.01978 -0.00990 -7.40371; 0.01736 1.25162 0.09207 -30.65387; 0.00901 -0.09086 0.99432 -0.86733; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.06481 -0.01978 -0.00990 -7.40371; 0.01736 1.25162 0.09207 -30.65387; 0.00901 -0.09086 0.99432 -0.86733; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 6842.8 after pass:transform: ( 1.06, -0.02, -0.01, -7.40) ( 0.02, 1.25, 0.09, -30.65) ( 0.01, -0.09, 0.99, -0.87) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 6842.8 tol 0.000010 Resulting transform: 1.065 -0.020 -0.010 -7.404; 0.017 1.252 0.092 -30.654; 0.009 -0.091 0.994 -0.867; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -6842.9 (old=-7447.8) transform before final EM align: 1.065 -0.020 -0.010 -7.404; 0.017 1.252 0.092 -30.654; 0.009 -0.091 0.994 -0.867; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06481 -0.01978 -0.00990 -7.40371; 0.01736 1.25162 0.09207 -30.65387; 0.00901 -0.09086 0.99432 -0.86733; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.06481 -0.01978 -0.00990 -7.40371; 0.01736 1.25162 0.09207 -30.65387; 0.00901 -0.09086 0.99432 -0.86733; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 830599.0 after pass:transform: ( 1.06, -0.02, -0.01, -7.40) ( 0.02, 1.25, 0.09, -30.65) ( 0.01, -0.09, 0.99, -0.87) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... dfp_em_step_func: 011: -log(p) = 829640.0 after pass:transform: ( 1.07, -0.02, -0.01, -7.40) ( 0.02, 1.25, 0.09, -30.65) ( 0.01, -0.09, 0.99, -0.87) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... dfp_em_step_func: 012: -log(p) = 829639.9 after pass:transform: ( 1.07, -0.02, -0.01, -7.40) ( 0.02, 1.25, 0.09, -30.65) ( 0.01, -0.09, 0.99, -0.87) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 829639.9 tol 0.000000 final transform: 1.066 -0.019 -0.009 -7.404; 0.018 1.252 0.092 -30.654; 0.009 -0.091 0.995 -0.867; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 20 minutes and 17 seconds. #-------------------------------------- #@# CA Normalize Mon Mar 21 18:50:44 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (62, 49, 38) --> (194, 160, 203) using (106, 86, 121) as brain centroid... mean wm in atlas = 107, using box (90,72,101) --> (122, 99,141) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.066 -0.019 -0.009 -7.404; 0.018 1.252 0.092 -30.654; 0.009 -0.091 0.995 -0.867; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (190, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 225.0 0 of 36 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (128, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 225.0 0 of 64 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (175, 159, 115) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 225.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 123, 59) --> (128, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 225.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 118, 96) --> (144, 173, 127) Brain_Stem: limiting intensities to 86.0 --> 225.0 0 of 7 (0.0%) samples deleted using 124 total control points for intensity normalization... bias field = 0.990 +- 0.065 0 of 124 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (190, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 208.0 0 of 93 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (128, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 208.0 0 of 108 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (175, 159, 115) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 208.0 0 of 34 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 123, 59) --> (128, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 208.0 0 of 65 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 118, 96) --> (144, 173, 127) Brain_Stem: limiting intensities to 73.0 --> 208.0 0 of 78 (0.0%) samples deleted using 378 total control points for intensity normalization... bias field = 0.996 +- 0.043 0 of 378 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (190, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 207.0 0 of 201 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (128, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 207.0 0 of 226 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (175, 159, 115) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 207.0 0 of 78 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 123, 59) --> (128, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 207.0 0 of 70 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 118, 96) --> (144, 173, 127) Brain_Stem: limiting intensities to 78.0 --> 207.0 18 of 100 (18.0%) samples deleted using 675 total control points for intensity normalization... bias field = 1.001 +- 0.036 0 of 657 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 58 seconds. #-------------------------------------- #@# CA Reg Mon Mar 21 18:52:44 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.34 (predicted orig area = 6.0) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.895, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44385.191 ms 0001: dt=129.472000, rms=0.849 (5.137%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43412.477 ms 0002: dt=129.472000, rms=0.819 (3.560%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46655.809 ms 0003: dt=110.976000, rms=0.813 (0.636%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46512.129 ms 0004: dt=221.952000, rms=0.798 (1.848%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43926.098 ms 0005: dt=32.368000, rms=0.796 (0.310%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46756.941 ms 0006: dt=73.984000, rms=0.794 (0.237%), neg=0, invalid=766 0007: dt=73.984000, rms=0.791 (0.346%), neg=0, invalid=766 0008: dt=73.984000, rms=0.787 (0.542%), neg=0, invalid=766 0009: dt=73.984000, rms=0.782 (0.635%), neg=0, invalid=766 0010: dt=73.984000, rms=0.777 (0.627%), neg=0, invalid=766 0011: dt=73.984000, rms=0.772 (0.630%), neg=0, invalid=766 0012: dt=73.984000, rms=0.767 (0.628%), neg=0, invalid=766 0013: dt=73.984000, rms=0.763 (0.574%), neg=0, invalid=766 0014: dt=73.984000, rms=0.759 (0.465%), neg=0, invalid=766 0015: dt=73.984000, rms=0.756 (0.422%), neg=0, invalid=766 0016: dt=73.984000, rms=0.753 (0.436%), neg=0, invalid=766 0017: dt=73.984000, rms=0.749 (0.476%), neg=0, invalid=766 0018: dt=73.984000, rms=0.746 (0.498%), neg=0, invalid=766 0019: dt=73.984000, rms=0.742 (0.472%), neg=0, invalid=766 0020: dt=73.984000, rms=0.739 (0.407%), neg=0, invalid=766 0021: dt=73.984000, rms=0.736 (0.366%), neg=0, invalid=766 0022: dt=73.984000, rms=0.733 (0.385%), neg=0, invalid=766 0023: dt=73.984000, rms=0.731 (0.392%), neg=0, invalid=766 0024: dt=73.984000, rms=0.728 (0.366%), neg=0, invalid=766 0025: dt=73.984000, rms=0.726 (0.301%), neg=0, invalid=766 0026: dt=73.984000, rms=0.724 (0.259%), neg=0, invalid=766 0027: dt=73.984000, rms=0.722 (0.254%), neg=0, invalid=766 0028: dt=73.984000, rms=0.720 (0.288%), neg=0, invalid=766 0029: dt=73.984000, rms=0.718 (0.312%), neg=0, invalid=766 0030: dt=73.984000, rms=0.716 (0.278%), neg=0, invalid=766 0031: dt=73.984000, rms=0.714 (0.207%), neg=0, invalid=766 0032: dt=73.984000, rms=0.713 (0.160%), neg=0, invalid=766 0033: dt=73.984000, rms=0.712 (0.202%), neg=0, invalid=766 0034: dt=73.984000, rms=0.710 (0.239%), neg=0, invalid=766 0035: dt=73.984000, rms=0.708 (0.206%), neg=0, invalid=766 0036: dt=73.984000, rms=0.708 (0.122%), neg=0, invalid=766 0037: dt=73.984000, rms=0.707 (0.085%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43259.789 ms 0038: dt=517.888000, rms=0.705 (0.289%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41037.020 ms 0039: dt=0.000000, rms=0.705 (-0.011%), neg=0, invalid=766 0040: dt=0.850000, rms=0.705 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43466.766 ms 0041: dt=0.289000, rms=0.705 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41466.184 ms 0042: dt=0.000000, rms=0.705 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41406.309 ms 0043: dt=0.000000, rms=0.705 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.713, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39269.449 ms 0044: dt=124.416000, rms=0.705 (1.169%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45769.188 ms 0045: dt=40.987406, rms=0.687 (2.458%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38456.465 ms 0046: dt=9.072000, rms=0.686 (0.199%), neg=0, invalid=766 0047: dt=9.072000, rms=0.685 (0.151%), neg=0, invalid=766 0048: dt=9.072000, rms=0.684 (0.154%), neg=0, invalid=766 0049: dt=9.072000, rms=0.682 (0.224%), neg=0, invalid=766 0050: dt=9.072000, rms=0.680 (0.390%), neg=0, invalid=766 0051: dt=9.072000, rms=0.676 (0.585%), neg=0, invalid=766 0052: dt=9.072000, rms=0.671 (0.709%), neg=0, invalid=766 0053: dt=9.072000, rms=0.666 (0.695%), neg=0, invalid=766 0054: dt=9.072000, rms=0.662 (0.622%), neg=0, invalid=766 0055: dt=9.072000, rms=0.658 (0.568%), neg=0, invalid=766 0056: dt=9.072000, rms=0.655 (0.531%), neg=0, invalid=766 0057: dt=9.072000, rms=0.652 (0.461%), neg=0, invalid=766 0058: dt=9.072000, rms=0.649 (0.408%), neg=0, invalid=766 0059: dt=9.072000, rms=0.646 (0.426%), neg=0, invalid=766 0060: dt=9.072000, rms=0.643 (0.469%), neg=0, invalid=766 0061: dt=9.072000, rms=0.640 (0.488%), neg=0, invalid=766 0062: dt=9.072000, rms=0.637 (0.439%), neg=0, invalid=766 0063: dt=9.072000, rms=0.635 (0.368%), neg=0, invalid=766 0064: dt=9.072000, rms=0.633 (0.324%), neg=0, invalid=766 0065: dt=9.072000, rms=0.631 (0.292%), neg=0, invalid=766 0066: dt=9.072000, rms=0.629 (0.259%), neg=0, invalid=766 0067: dt=9.072000, rms=0.628 (0.222%), neg=0, invalid=766 0068: dt=9.072000, rms=0.627 (0.202%), neg=0, invalid=766 0069: dt=9.072000, rms=0.625 (0.218%), neg=0, invalid=766 0070: dt=9.072000, rms=0.624 (0.234%), neg=0, invalid=766 0071: dt=9.072000, rms=0.623 (0.224%), neg=0, invalid=766 0072: dt=9.072000, rms=0.621 (0.198%), neg=0, invalid=766 0073: dt=9.072000, rms=0.620 (0.163%), neg=0, invalid=766 0074: dt=9.072000, rms=0.619 (0.138%), neg=0, invalid=766 0075: dt=9.072000, rms=0.619 (0.116%), neg=0, invalid=766 0076: dt=9.072000, rms=0.618 (0.104%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49694.414 ms 0077: dt=145.152000, rms=0.617 (0.110%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42978.207 ms 0078: dt=9.072000, rms=0.617 (0.026%), neg=0, invalid=766 0079: dt=9.072000, rms=0.617 (0.015%), neg=0, invalid=766 0080: dt=9.072000, rms=0.617 (0.001%), neg=0, invalid=766 0081: dt=9.072000, rms=0.617 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43409.961 ms 0082: dt=36.288000, rms=0.617 (0.042%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45620.086 ms 0083: dt=31.104000, rms=0.617 (0.012%), neg=0, invalid=766 0084: dt=31.104000, rms=0.617 (0.001%), neg=0, invalid=766 0085: dt=31.104000, rms=0.617 (-0.044%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43526.176 ms 0086: dt=5.423729, rms=0.644 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40919.074 ms 0087: dt=2.800000, rms=0.644 (0.009%), neg=0, invalid=766 0088: dt=2.800000, rms=0.644 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44633.328 ms 0089: dt=0.000000, rms=0.644 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49062.285 ms 0090: dt=4.684685, rms=0.705 (1.949%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48187.500 ms 0091: dt=1.008000, rms=0.704 (0.051%), neg=0, invalid=766 0092: dt=1.008000, rms=0.704 (0.011%), neg=0, invalid=766 0093: dt=1.008000, rms=0.704 (-0.065%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49344.988 ms 0094: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.792, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44898.055 ms 0095: dt=0.867368, rms=0.789 (0.363%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54584.605 ms 0096: dt=1.566502, rms=0.786 (0.482%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46579.492 ms 0097: dt=1.380000, rms=0.784 (0.187%), neg=0, invalid=766 0098: dt=1.380000, rms=0.784 (0.062%), neg=0, invalid=766 0099: dt=1.380000, rms=0.784 (-0.228%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.784, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44275.934 ms 0100: dt=1.024000, rms=0.783 (0.140%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41628.211 ms 0101: dt=0.000000, rms=0.783 (-0.005%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44086.945 ms 0102: dt=0.448000, rms=0.695 (3.204%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38747.371 ms 0103: dt=0.000000, rms=0.695 (0.013%), neg=0, invalid=766 0104: dt=0.050000, rms=0.695 (-0.419%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37614.980 ms 0105: dt=0.000000, rms=0.695 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.17621 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (2331 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2331 voxels, peak = 4), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.12694 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (2058 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (2058 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.08720 (103) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (353 voxels, overlap=0.806) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (353 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.06688 (96) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (313 voxels, overlap=0.894) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (313 voxels, peak = 95), gca=94.6 gca peak = 0.24007 (63) mri peak = 0.06653 (57) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (561 voxels, overlap=0.948) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (561 voxels, peak = 58), gca=58.3 gca peak = 0.29892 (64) mri peak = 0.08851 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (567 voxels, overlap=0.928) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (567 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.08222 (105) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (57453 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (57453 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.08437 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (59226 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (59226 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03629 (59) Left_Cerebral_Cortex (3): linear fit = 0.93 x + 0.0 (19062 voxels, overlap=0.714) Left_Cerebral_Cortex (3): linear fit = 0.93 x + 0.0 (19062 voxels, peak = 58), gca=58.3 gca peak = 0.13270 (63) mri peak = 0.03515 (58) Right_Cerebral_Cortex (42): linear fit = 0.93 x + 0.0 (19836 voxels, overlap=0.639) Right_Cerebral_Cortex (42): linear fit = 0.93 x + 0.0 (19836 voxels, peak = 58), gca=58.3 gca peak = 0.15182 (70) mri peak = 0.10501 (65) Right_Caudate (50): linear fit = 0.88 x + 0.0 (259 voxels, overlap=0.028) Right_Caudate (50): linear fit = 0.88 x + 0.0 (259 voxels, peak = 61), gca=61.2 gca peak = 0.14251 (76) mri peak = 0.10013 (66) Left_Caudate (11): linear fit = 0.85 x + 0.0 (799 voxels, overlap=0.250) Left_Caudate (11): linear fit = 0.85 x + 0.0 (799 voxels, peak = 65), gca=64.6 gca peak = 0.12116 (60) mri peak = 0.04260 (56) Left_Cerebellum_Cortex (8): linear fit = 0.90 x + 0.0 (22813 voxels, overlap=0.618) Left_Cerebellum_Cortex (8): linear fit = 0.90 x + 0.0 (22813 voxels, peak = 54), gca=54.0 gca peak = 0.12723 (61) mri peak = 0.03999 (56) Right_Cerebellum_Cortex (47): linear fit = 0.90 x + 0.0 (26324 voxels, overlap=0.844) Right_Cerebellum_Cortex (47): linear fit = 0.90 x + 0.0 (26324 voxels, peak = 55), gca=54.9 gca peak = 0.22684 (88) mri peak = 0.08085 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7198 voxels, overlap=0.581) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7198 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.09394 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6994 voxels, overlap=0.617) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6994 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.10963 (56) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, overlap=0.832) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.12259 (58) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (327 voxels, overlap=0.859) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (327 voxels, peak = 57), gca=57.4 gca peak = 0.10129 (93) mri peak = 0.05663 (90) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4538 voxels, overlap=0.835) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4538 voxels, peak = 88), gca=88.3 gca peak = 0.12071 (89) mri peak = 0.05552 (88) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3337 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3337 voxels, peak = 87), gca=86.8 gca peak = 0.13716 (82) mri peak = 0.06422 (81) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2236 voxels, overlap=0.879) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2236 voxels, peak = 78), gca=77.9 gca peak = 0.15214 (84) mri peak = 0.05021 (79) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2158 voxels, overlap=0.863) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2158 voxels, peak = 80), gca=79.8 gca peak = 0.08983 (85) mri peak = 0.06019 (90) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10784 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10784 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.08755 (103) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (897 voxels, overlap=0.445) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (897 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.07676 (102) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1073 voxels, overlap=0.757) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1073 voxels, peak = 99), gca=98.7 gca peak = 0.21100 (36) mri peak = 0.23538 (12) gca peak = 0.13542 (27) mri peak = 0.18026 ( 7) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (477 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (477 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.92 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.715, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41873.047 ms 0106: dt=129.472000, rms=0.707 (1.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41873.559 ms 0107: dt=295.936000, rms=0.702 (0.809%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39248.438 ms 0108: dt=32.368000, rms=0.700 (0.242%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41758.195 ms 0109: dt=73.984000, rms=0.699 (0.118%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44413.422 ms 0110: dt=443.904000, rms=0.695 (0.552%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39676.613 ms 0111: dt=32.368000, rms=0.694 (0.119%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39868.191 ms 0112: dt=23.120000, rms=0.694 (0.014%), neg=0, invalid=766 0113: dt=23.120000, rms=0.694 (0.006%), neg=0, invalid=766 0114: dt=23.120000, rms=0.694 (0.013%), neg=0, invalid=766 0115: dt=23.120000, rms=0.694 (0.028%), neg=0, invalid=766 0116: dt=23.120000, rms=0.694 (0.055%), neg=0, invalid=766 0117: dt=23.120000, rms=0.693 (0.092%), neg=0, invalid=766 0118: dt=23.120000, rms=0.692 (0.112%), neg=0, invalid=766 0119: dt=23.120000, rms=0.691 (0.113%), neg=0, invalid=766 0120: dt=23.120000, rms=0.691 (0.099%), neg=0, invalid=766 0121: dt=23.120000, rms=0.690 (0.091%), neg=0, invalid=766 0122: dt=23.120000, rms=0.690 (0.082%), neg=0, invalid=766 0123: dt=23.120000, rms=0.689 (0.076%), neg=0, invalid=766 0124: dt=23.120000, rms=0.688 (0.084%), neg=0, invalid=766 0125: dt=23.120000, rms=0.688 (0.091%), neg=0, invalid=766 0126: dt=23.120000, rms=0.687 (0.101%), neg=0, invalid=766 0127: dt=23.120000, rms=0.686 (0.105%), neg=0, invalid=766 0128: dt=23.120000, rms=0.686 (0.103%), neg=0, invalid=766 0129: dt=23.120000, rms=0.685 (0.097%), neg=0, invalid=766 0130: dt=23.120000, rms=0.684 (0.087%), neg=0, invalid=766 0131: dt=23.120000, rms=0.684 (0.080%), neg=0, invalid=766 0132: dt=23.120000, rms=0.683 (0.073%), neg=0, invalid=766 0133: dt=23.120000, rms=0.683 (0.069%), neg=0, invalid=766 0134: dt=23.120000, rms=0.682 (0.066%), neg=0, invalid=766 0135: dt=23.120000, rms=0.682 (0.074%), neg=0, invalid=766 0136: dt=23.120000, rms=0.681 (0.081%), neg=0, invalid=766 0137: dt=23.120000, rms=0.681 (0.081%), neg=0, invalid=766 0138: dt=23.120000, rms=0.680 (0.079%), neg=0, invalid=766 0139: dt=23.120000, rms=0.680 (0.074%), neg=0, invalid=766 0140: dt=23.120000, rms=0.679 (0.069%), neg=0, invalid=766 0141: dt=23.120000, rms=0.679 (0.063%), neg=0, invalid=766 0142: dt=23.120000, rms=0.678 (0.060%), neg=0, invalid=766 0143: dt=23.120000, rms=0.678 (0.056%), neg=0, invalid=766 0144: dt=23.120000, rms=0.678 (0.063%), neg=0, invalid=766 0145: dt=23.120000, rms=0.677 (0.068%), neg=0, invalid=766 0146: dt=23.120000, rms=0.677 (0.070%), neg=0, invalid=766 0147: dt=23.120000, rms=0.676 (0.069%), neg=0, invalid=766 0148: dt=23.120000, rms=0.676 (0.069%), neg=0, invalid=766 0149: dt=23.120000, rms=0.675 (0.060%), neg=0, invalid=766 0150: dt=23.120000, rms=0.675 (0.054%), neg=0, invalid=766 0151: dt=23.120000, rms=0.675 (0.046%), neg=0, invalid=766 0152: dt=23.120000, rms=0.674 (0.048%), neg=0, invalid=766 0153: dt=23.120000, rms=0.674 (0.053%), neg=0, invalid=766 0154: dt=23.120000, rms=0.674 (0.058%), neg=0, invalid=766 0155: dt=23.120000, rms=0.673 (0.066%), neg=0, invalid=766 0156: dt=23.120000, rms=0.673 (0.061%), neg=0, invalid=766 0157: dt=23.120000, rms=0.672 (0.052%), neg=0, invalid=766 0158: dt=23.120000, rms=0.672 (0.047%), neg=0, invalid=766 0159: dt=23.120000, rms=0.672 (0.043%), neg=0, invalid=766 0160: dt=23.120000, rms=0.672 (0.043%), neg=0, invalid=766 0161: dt=23.120000, rms=0.671 (0.043%), neg=0, invalid=766 0162: dt=23.120000, rms=0.671 (0.045%), neg=0, invalid=766 0163: dt=23.120000, rms=0.671 (0.049%), neg=0, invalid=766 0164: dt=23.120000, rms=0.670 (0.048%), neg=0, invalid=766 0165: dt=23.120000, rms=0.670 (0.045%), neg=0, invalid=766 0166: dt=23.120000, rms=0.670 (0.042%), neg=0, invalid=766 0167: dt=23.120000, rms=0.669 (0.039%), neg=0, invalid=766 0168: dt=23.120000, rms=0.669 (0.035%), neg=0, invalid=766 0169: dt=23.120000, rms=0.669 (0.032%), neg=0, invalid=766 0170: dt=23.120000, rms=0.669 (0.034%), neg=0, invalid=766 0171: dt=23.120000, rms=0.669 (0.038%), neg=0, invalid=766 0172: dt=23.120000, rms=0.668 (0.039%), neg=0, invalid=766 0173: dt=23.120000, rms=0.668 (0.038%), neg=0, invalid=766 0174: dt=23.120000, rms=0.668 (0.036%), neg=0, invalid=766 0175: dt=23.120000, rms=0.668 (0.032%), neg=0, invalid=766 0176: dt=23.120000, rms=0.667 (0.030%), neg=0, invalid=766 0177: dt=23.120000, rms=0.667 (0.030%), neg=0, invalid=766 0178: dt=23.120000, rms=0.667 (0.032%), neg=0, invalid=766 0179: dt=23.120000, rms=0.667 (0.033%), neg=0, invalid=766 0180: dt=23.120000, rms=0.666 (0.031%), neg=0, invalid=766 0181: dt=23.120000, rms=0.666 (0.030%), neg=0, invalid=766 0182: dt=23.120000, rms=0.666 (0.027%), neg=0, invalid=766 0183: dt=23.120000, rms=0.666 (0.025%), neg=0, invalid=766 0184: dt=23.120000, rms=0.666 (0.025%), neg=0, invalid=766 0185: dt=23.120000, rms=0.666 (0.026%), neg=0, invalid=766 0186: dt=23.120000, rms=0.665 (0.028%), neg=0, invalid=766 0187: dt=23.120000, rms=0.665 (0.028%), neg=0, invalid=766 0188: dt=23.120000, rms=0.665 (0.027%), neg=0, invalid=766 0189: dt=23.120000, rms=0.665 (0.024%), neg=0, invalid=766 0190: dt=23.120000, rms=0.665 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44371.918 ms 0191: dt=3551.232000, rms=0.664 (0.117%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42565.727 ms 0192: dt=110.976000, rms=0.662 (0.239%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41516.816 ms 0193: dt=13.872000, rms=0.662 (0.002%), neg=0, invalid=766 0194: dt=13.872000, rms=0.662 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43032.285 ms 0195: dt=27.744000, rms=0.662 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49872.453 ms 0196: dt=55.488000, rms=0.662 (0.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51911.496 ms 0197: dt=443.904000, rms=0.660 (0.266%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53273.086 ms 0198: dt=32.368000, rms=0.660 (0.012%), neg=0, invalid=766 0199: dt=32.368000, rms=0.660 (0.011%), neg=0, invalid=766 0200: dt=32.368000, rms=0.660 (0.020%), neg=0, invalid=766 0201: dt=32.368000, rms=0.660 (0.032%), neg=0, invalid=766 0202: dt=32.368000, rms=0.660 (0.042%), neg=0, invalid=766 0203: dt=32.368000, rms=0.659 (0.048%), neg=0, invalid=766 0204: dt=32.368000, rms=0.659 (0.043%), neg=0, invalid=766 0205: dt=32.368000, rms=0.659 (0.033%), neg=0, invalid=766 0206: dt=32.368000, rms=0.659 (0.019%), neg=0, invalid=766 0207: dt=32.368000, rms=0.658 (0.014%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65827.609 ms 0208: dt=295.936000, rms=0.658 (0.015%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65020.332 ms 0209: dt=517.888000, rms=0.658 (0.091%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61083.879 ms 0210: dt=8.092000, rms=0.658 (0.002%), neg=0, invalid=766 0211: dt=8.092000, rms=0.658 (0.001%), neg=0, invalid=766 0212: dt=8.092000, rms=0.658 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.658, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55034.641 ms 0213: dt=145.152000, rms=0.646 (1.860%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58785.836 ms 0214: dt=82.944000, rms=0.638 (1.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44166.797 ms 0215: dt=20.736000, rms=0.636 (0.355%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48485.586 ms 0216: dt=145.152000, rms=0.629 (1.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43433.031 ms 0217: dt=20.736000, rms=0.627 (0.442%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51327.711 ms 0218: dt=145.152000, rms=0.621 (0.825%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43719.980 ms 0219: dt=25.920000, rms=0.620 (0.283%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48162.469 ms 0220: dt=62.208000, rms=0.617 (0.428%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44777.074 ms 0221: dt=20.736000, rms=0.616 (0.129%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51177.918 ms 0222: dt=497.664000, rms=0.606 (1.719%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39130.766 ms 0223: dt=0.567000, rms=0.606 (0.002%), neg=0, invalid=766 0224: dt=0.035437, rms=0.606 (0.004%), neg=0, invalid=766 0225: dt=0.017719, rms=0.606 (0.001%), neg=0, invalid=766 0226: dt=0.004430, rms=0.606 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49959.328 ms 0227: dt=0.001898, rms=0.606 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24798.850 ms 0228: dt=0.000000, rms=0.606 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.610, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27193.012 ms 0229: dt=0.000000, rms=0.610 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.610, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27674.973 ms 0230: dt=0.000000, rms=0.610 (0.000%), neg=0, invalid=766 0231: dt=0.000015, rms=0.610 (0.000%), neg=0, invalid=766 0232: dt=0.000008, rms=0.610 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.625, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23478.258 ms 0233: dt=0.000000, rms=0.625 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.625, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25134.969 ms 0234: dt=0.000000, rms=0.625 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.655, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56504.566 ms 0235: dt=0.448000, rms=0.648 (1.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54574.805 ms 0236: dt=0.448000, rms=0.642 (0.918%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53991.543 ms 0237: dt=0.448000, rms=0.637 (0.798%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56147.250 ms 0238: dt=0.448000, rms=0.632 (0.697%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62195.863 ms 0239: dt=1.792000, rms=0.618 (2.348%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61653.719 ms 0240: dt=1.792000, rms=0.610 (1.263%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58536.809 ms 0241: dt=1.792000, rms=0.605 (0.726%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57626.004 ms 0242: dt=1.792000, rms=0.602 (0.481%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55152.012 ms 0243: dt=0.448000, rms=0.602 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55532.426 ms 0244: dt=1.792000, rms=0.600 (0.310%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54536.898 ms 0245: dt=1.792000, rms=0.599 (0.229%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53986.293 ms 0246: dt=1.536000, rms=0.598 (0.150%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50026.328 ms 0247: dt=0.607143, rms=0.598 (0.047%), neg=0, invalid=766 0248: dt=0.607143, rms=0.597 (0.050%), neg=0, invalid=766 0249: dt=0.607143, rms=0.597 (0.084%), neg=0, invalid=766 0250: dt=0.607143, rms=0.596 (0.111%), neg=0, invalid=766 0251: dt=0.303571, rms=0.596 (0.019%), neg=0, invalid=766 0252: dt=0.303571, rms=0.596 (0.030%), neg=0, invalid=766 0253: dt=0.303571, rms=0.596 (0.044%), neg=0, invalid=766 0254: dt=0.303571, rms=0.595 (0.047%), neg=0, invalid=766 0255: dt=0.303571, rms=0.595 (0.051%), neg=0, invalid=766 0256: dt=0.303571, rms=0.595 (0.055%), neg=0, invalid=766 0257: dt=0.303571, rms=0.594 (0.054%), neg=0, invalid=766 0258: dt=0.303571, rms=0.594 (0.046%), neg=0, invalid=766 0259: dt=0.303571, rms=0.594 (0.045%), neg=0, invalid=766 0260: dt=0.303571, rms=0.594 (0.037%), neg=0, invalid=766 0261: dt=0.303571, rms=0.593 (0.032%), neg=0, invalid=766 0262: dt=0.303571, rms=0.593 (0.022%), neg=0, invalid=766 0263: dt=0.303571, rms=0.593 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62585.285 ms 0264: dt=1.792000, rms=0.593 (0.005%), neg=0, invalid=766 0265: dt=1.792000, rms=0.593 (0.013%), neg=0, invalid=766 0266: dt=1.792000, rms=0.593 (0.032%), neg=0, invalid=766 0267: dt=1.792000, rms=0.593 (0.049%), neg=0, invalid=766 0268: dt=1.792000, rms=0.592 (0.061%), neg=0, invalid=766 0269: dt=1.792000, rms=0.592 (0.016%), neg=0, invalid=766 0270: dt=1.792000, rms=0.592 (0.019%), neg=0, invalid=766 0271: dt=1.792000, rms=0.592 (0.031%), neg=0, invalid=766 0272: dt=1.792000, rms=0.592 (0.038%), neg=0, invalid=766 0273: dt=1.792000, rms=0.591 (0.043%), neg=0, invalid=766 0274: dt=1.792000, rms=0.591 (0.027%), neg=0, invalid=766 0275: dt=1.792000, rms=0.591 (0.013%), neg=0, invalid=766 0276: dt=1.792000, rms=0.591 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58839.020 ms 0277: dt=1.280000, rms=0.591 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46881.551 ms 0278: dt=1.536000, rms=0.591 (0.002%), neg=0, invalid=766 0279: dt=1.536000, rms=0.591 (0.002%), neg=0, invalid=766 0280: dt=1.536000, rms=0.591 (0.009%), neg=0, invalid=766 0281: dt=1.536000, rms=0.591 (0.016%), neg=0, invalid=766 0282: dt=1.536000, rms=0.591 (0.024%), neg=0, invalid=766 0283: dt=1.536000, rms=0.591 (0.026%), neg=0, invalid=766 0284: dt=1.536000, rms=0.590 (0.030%), neg=0, invalid=766 0285: dt=1.536000, rms=0.590 (0.033%), neg=0, invalid=766 0286: dt=1.536000, rms=0.590 (0.031%), neg=0, invalid=766 0287: dt=1.536000, rms=0.590 (0.026%), neg=0, invalid=766 0288: dt=1.536000, rms=0.590 (0.020%), neg=0, invalid=766 0289: dt=1.536000, rms=0.590 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49488.625 ms 0290: dt=0.448000, rms=0.590 (0.002%), neg=0, invalid=766 0291: dt=0.448000, rms=0.590 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49160.172 ms 0292: dt=1.792000, rms=0.588 (0.227%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47254.977 ms 0293: dt=1.792000, rms=0.588 (0.091%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48083.723 ms 0294: dt=3.000000, rms=0.587 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48427.262 ms 0295: dt=5.120000, rms=0.587 (0.044%), neg=0, invalid=766 0296: dt=0.640000, rms=0.587 (0.001%), neg=0, invalid=766 0297: dt=0.640000, rms=0.587 (0.011%), neg=0, invalid=766 0298: dt=0.640000, rms=0.587 (0.002%), neg=0, invalid=766 0299: dt=0.640000, rms=0.587 (0.013%), neg=0, invalid=766 0300: dt=0.640000, rms=0.587 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48300.738 ms 0301: dt=1.792000, rms=0.587 (0.013%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.575, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48976.910 ms 0302: dt=0.384000, rms=0.556 (3.339%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41123.512 ms 0303: dt=0.028000, rms=0.556 (0.097%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49930.672 ms 0304: dt=0.448000, rms=0.548 (1.381%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46770.883 ms 0305: dt=0.080000, rms=0.547 (0.121%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45081.742 ms 0306: dt=0.112000, rms=0.546 (0.172%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49109.438 ms 0307: dt=0.448000, rms=0.543 (0.618%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46385.449 ms 0308: dt=0.448000, rms=0.541 (0.427%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35299.277 ms 0309: dt=0.028000, rms=0.541 (0.019%), neg=0, invalid=766 0310: dt=0.028000, rms=0.540 (0.021%), neg=0, invalid=766 0311: dt=0.028000, rms=0.540 (0.039%), neg=0, invalid=766 0312: dt=0.028000, rms=0.540 (0.053%), neg=0, invalid=766 0313: dt=0.028000, rms=0.540 (0.068%), neg=0, invalid=766 0314: dt=0.028000, rms=0.539 (0.080%), neg=0, invalid=766 0315: dt=0.028000, rms=0.539 (0.087%), neg=0, invalid=766 0316: dt=0.028000, rms=0.539 (0.015%), neg=0, invalid=766 0317: dt=0.028000, rms=0.538 (0.029%), neg=0, invalid=766 0318: dt=0.028000, rms=0.538 (0.043%), neg=0, invalid=766 0319: dt=0.028000, rms=0.538 (0.051%), neg=0, invalid=766 0320: dt=0.028000, rms=0.538 (0.064%), neg=0, invalid=766 0321: dt=0.028000, rms=0.537 (0.068%), neg=0, invalid=766 0322: dt=0.028000, rms=0.537 (0.073%), neg=0, invalid=766 0323: dt=0.028000, rms=0.536 (0.077%), neg=0, invalid=766 0324: dt=0.028000, rms=0.536 (0.081%), neg=0, invalid=766 0325: dt=0.028000, rms=0.536 (0.081%), neg=0, invalid=766 0326: dt=0.028000, rms=0.535 (0.083%), neg=0, invalid=766 0327: dt=0.028000, rms=0.535 (0.082%), neg=0, invalid=766 0328: dt=0.028000, rms=0.534 (0.083%), neg=0, invalid=766 0329: dt=0.028000, rms=0.534 (0.077%), neg=0, invalid=766 0330: dt=0.028000, rms=0.533 (0.076%), neg=0, invalid=766 0331: dt=0.028000, rms=0.533 (0.075%), neg=0, invalid=766 0332: dt=0.028000, rms=0.533 (0.069%), neg=0, invalid=766 0333: dt=0.028000, rms=0.532 (0.067%), neg=0, invalid=766 0334: dt=0.028000, rms=0.532 (0.064%), neg=0, invalid=766 0335: dt=0.028000, rms=0.532 (0.061%), neg=0, invalid=766 0336: dt=0.028000, rms=0.531 (0.052%), neg=0, invalid=766 0337: dt=0.028000, rms=0.531 (0.054%), neg=0, invalid=766 0338: dt=0.028000, rms=0.531 (0.045%), neg=0, invalid=766 0339: dt=0.028000, rms=0.531 (0.048%), neg=0, invalid=766 0340: dt=0.028000, rms=0.530 (0.041%), neg=0, invalid=766 0341: dt=0.028000, rms=0.530 (0.040%), neg=0, invalid=766 0342: dt=0.028000, rms=0.530 (0.035%), neg=0, invalid=766 0343: dt=0.028000, rms=0.530 (0.031%), neg=0, invalid=766 0344: dt=0.028000, rms=0.530 (0.031%), neg=0, invalid=766 0345: dt=0.028000, rms=0.529 (0.027%), neg=0, invalid=766 0346: dt=0.028000, rms=0.529 (0.026%), neg=0, invalid=766 0347: dt=0.028000, rms=0.529 (0.022%), neg=0, invalid=766 0348: dt=0.028000, rms=0.529 (0.022%), neg=0, invalid=766 0349: dt=0.028000, rms=0.529 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39721.125 ms 0350: dt=0.320000, rms=0.529 (0.006%), neg=0, invalid=766 0351: dt=0.320000, rms=0.529 (0.004%), neg=0, invalid=766 0352: dt=0.160000, rms=0.529 (0.007%), neg=0, invalid=766 0353: dt=0.160000, rms=0.529 (0.005%), neg=0, invalid=766 0354: dt=0.160000, rms=0.529 (0.005%), neg=0, invalid=766 0355: dt=0.160000, rms=0.529 (0.006%), neg=0, invalid=766 0356: dt=0.080000, rms=0.529 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37306.996 ms 0357: dt=0.112000, rms=0.527 (0.261%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39857.266 ms 0358: dt=0.448000, rms=0.524 (0.741%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34624.098 ms 0359: dt=0.000000, rms=0.524 (-0.002%), neg=0, invalid=766 0360: dt=0.050000, rms=0.524 (-0.002%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.520, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44803.277 ms iter 0, gcam->neg = 22 after 21 iterations, nbhd size=2, neg = 0 0361: dt=44.800000, rms=0.501 (3.621%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52922.281 ms iter 0, gcam->neg = 42 after 23 iterations, nbhd size=2, neg = 0 0362: dt=44.800000, rms=0.495 (1.262%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59298.746 ms iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0363: dt=7.496855, rms=0.494 (0.204%), neg=0, invalid=766 0364: dt=7.496855, rms=0.493 (0.163%), neg=0, invalid=766 0365: dt=7.496855, rms=0.492 (0.179%), neg=0, invalid=766 0366: dt=7.496855, rms=0.491 (0.243%), neg=0, invalid=766 0367: dt=7.496855, rms=0.490 (0.250%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0368: dt=7.496855, rms=0.489 (0.280%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0369: dt=7.496855, rms=0.487 (0.301%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0370: dt=7.496855, rms=0.486 (0.278%), neg=0, invalid=766 0371: dt=7.496855, rms=0.484 (0.264%), neg=0, invalid=766 0372: dt=7.496855, rms=0.483 (0.224%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0373: dt=7.496855, rms=0.482 (0.202%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0374: dt=7.496855, rms=0.481 (0.198%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0375: dt=7.496855, rms=0.481 (0.152%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0376: dt=7.496855, rms=0.480 (0.141%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0377: dt=7.496855, rms=0.479 (0.134%), neg=0, invalid=766 0378: dt=7.496855, rms=0.479 (0.133%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0379: dt=7.496855, rms=0.478 (0.145%), neg=0, invalid=766 0380: dt=7.496855, rms=0.477 (0.146%), neg=0, invalid=766 0381: dt=7.496855, rms=0.477 (0.129%), neg=0, invalid=766 0382: dt=7.496855, rms=0.476 (0.104%), neg=0, invalid=766 0383: dt=7.496855, rms=0.476 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56224.887 ms 0384: dt=11.200000, rms=0.476 (0.038%), neg=0, invalid=766 0385: dt=11.200000, rms=0.476 (0.020%), neg=0, invalid=766 0386: dt=11.200000, rms=0.475 (0.050%), neg=0, invalid=766 0387: dt=11.200000, rms=0.475 (0.058%), neg=0, invalid=766 0388: dt=11.200000, rms=0.475 (0.048%), neg=0, invalid=766 0389: dt=11.200000, rms=0.475 (0.065%), neg=0, invalid=766 0390: dt=11.200000, rms=0.474 (0.068%), neg=0, invalid=766 0391: dt=11.200000, rms=0.474 (0.045%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53063.887 ms 0392: dt=44.800000, rms=0.470 (0.860%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55152.691 ms 0393: dt=11.200000, rms=0.469 (0.169%), neg=0, invalid=766 0394: dt=11.200000, rms=0.469 (0.046%), neg=0, invalid=766 0395: dt=11.200000, rms=0.468 (0.128%), neg=0, invalid=766 0396: dt=11.200000, rms=0.468 (0.152%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0397: dt=11.200000, rms=0.467 (0.120%), neg=0, invalid=766 0398: dt=11.200000, rms=0.467 (0.047%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49622.605 ms 0399: dt=11.200000, rms=0.467 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49181.117 ms 0400: dt=4.800000, rms=0.467 (0.006%), neg=0, invalid=766 0401: dt=4.800000, rms=0.466 (0.005%), neg=0, invalid=766 0402: dt=4.800000, rms=0.466 (0.016%), neg=0, invalid=766 0403: dt=4.800000, rms=0.466 (0.017%), neg=0, invalid=766 0404: dt=4.800000, rms=0.466 (0.030%), neg=0, invalid=766 0405: dt=4.800000, rms=0.466 (0.026%), neg=0, invalid=766 0406: dt=4.800000, rms=0.466 (0.019%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51902.129 ms 0407: dt=1.008000, rms=0.476 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52102.305 ms 0408: dt=0.720000, rms=0.476 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52228.941 ms 0409: dt=1.935484, rms=0.476 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52232.418 ms 0410: dt=1.008000, rms=0.476 (0.005%), neg=0, invalid=766 0411: dt=1.008000, rms=0.476 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52969.887 ms 0412: dt=1.136929, rms=0.492 (0.241%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52435.066 ms 0413: dt=0.384000, rms=0.492 (0.006%), neg=0, invalid=766 0414: dt=0.384000, rms=0.492 (0.001%), neg=0, invalid=766 0415: dt=0.384000, rms=0.492 (-0.067%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52458.652 ms 0416: dt=1.074380, rms=0.491 (0.109%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52321.859 ms 0417: dt=0.448000, rms=0.491 (0.010%), neg=0, invalid=766 0418: dt=0.448000, rms=0.491 (0.000%), neg=0, invalid=766 0419: dt=0.448000, rms=0.491 (-0.046%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59493.574 ms iter 0, gcam->neg = 952 after 11 iterations, nbhd size=1, neg = 0 0420: dt=1.869649, rms=0.434 (8.738%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56624.266 ms 0421: dt=0.000188, rms=0.434 (-0.009%), neg=0, invalid=766 0422: dt=0.000188, rms=0.434 (0.000%), neg=0, invalid=766 0423: dt=0.000188, rms=0.434 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52166.043 ms 0424: dt=0.000375, rms=0.434 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52144.719 ms 0425: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56588.734 ms iter 0, gcam->neg = 315 after 12 iterations, nbhd size=1, neg = 0 0426: dt=0.376794, rms=0.411 (1.842%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58870.141 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0427: dt=0.007000, rms=0.411 (0.003%), neg=0, invalid=766 0428: dt=0.007000, rms=0.411 (0.011%), neg=0, invalid=766 0429: dt=0.007000, rms=0.411 (0.022%), neg=0, invalid=766 0430: dt=0.007000, rms=0.411 (0.030%), neg=0, invalid=766 0431: dt=0.007000, rms=0.410 (0.042%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0432: dt=0.007000, rms=0.410 (0.043%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0433: dt=0.007000, rms=0.410 (0.050%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0434: dt=0.007000, rms=0.410 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0435: dt=0.007000, rms=0.410 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0436: dt=0.007000, rms=0.409 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0437: dt=0.007000, rms=0.409 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0438: dt=0.007000, rms=0.409 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0439: dt=0.007000, rms=0.409 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0440: dt=0.007000, rms=0.408 (0.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60033.746 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0441: dt=0.001000, rms=0.409 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63012.957 ms iter 0, gcam->neg = 175 after 18 iterations, nbhd size=2, neg = 0 0442: dt=0.256000, rms=0.406 (0.575%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58160.613 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0443: dt=0.004000, rms=0.406 (-0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0444: dt=0.004000, rms=0.406 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0445: dt=0.004000, rms=0.406 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0446: dt=0.004000, rms=0.406 (0.018%), neg=0, invalid=766 0447: dt=0.004000, rms=0.406 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0448: dt=0.004000, rms=0.406 (0.022%), neg=0, invalid=766 0449: dt=0.004000, rms=0.406 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0450: dt=0.004000, rms=0.406 (0.027%), neg=0, invalid=766 0451: dt=0.004000, rms=0.406 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0452: dt=0.004000, rms=0.405 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0453: dt=0.004000, rms=0.405 (0.031%), neg=0, invalid=766 0454: dt=0.004000, rms=0.405 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0455: dt=0.004000, rms=0.405 (0.030%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58389.613 ms iter 0, gcam->neg = 108 after 16 iterations, nbhd size=2, neg = 0 0456: dt=0.112000, rms=0.402 (0.540%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64468.781 ms iter 0, gcam->neg = 12 after 6 iterations, nbhd size=1, neg = 0 0457: dt=0.019715, rms=0.402 (0.066%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0458: dt=0.019715, rms=0.401 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0459: dt=0.019715, rms=0.401 (0.135%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 0460: dt=0.019715, rms=0.400 (0.177%), neg=0, invalid=766 iter 0, gcam->neg = 29 after 14 iterations, nbhd size=2, neg = 0 0461: dt=0.019715, rms=0.399 (0.209%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 20 iterations, nbhd size=2, neg = 0 0462: dt=0.019715, rms=0.398 (0.229%), neg=0, invalid=766 iter 0, gcam->neg = 29 after 7 iterations, nbhd size=1, neg = 0 0463: dt=0.019715, rms=0.398 (0.235%), neg=0, invalid=766 iter 0, gcam->neg = 39 after 7 iterations, nbhd size=1, neg = 0 0464: dt=0.019715, rms=0.397 (0.230%), neg=0, invalid=766 iter 0, gcam->neg = 49 after 16 iterations, nbhd size=2, neg = 0 0465: dt=0.019715, rms=0.396 (0.217%), neg=0, invalid=766 iter 0, gcam->neg = 59 after 15 iterations, nbhd size=2, neg = 0 0466: dt=0.019715, rms=0.395 (0.205%), neg=0, invalid=766 iter 0, gcam->neg = 81 after 18 iterations, nbhd size=2, neg = 0 0467: dt=0.019715, rms=0.394 (0.174%), neg=0, invalid=766 iter 0, gcam->neg = 87 after 9 iterations, nbhd size=1, neg = 0 0468: dt=0.019715, rms=0.394 (0.165%), neg=0, invalid=766 iter 0, gcam->neg = 98 after 16 iterations, nbhd size=2, neg = 0 0469: dt=0.019715, rms=0.393 (0.132%), neg=0, invalid=766 iter 0, gcam->neg = 117 after 9 iterations, nbhd size=1, neg = 0 0470: dt=0.019715, rms=0.393 (0.112%), neg=0, invalid=766 iter 0, gcam->neg = 127 after 27 iterations, nbhd size=3, neg = 0 0471: dt=0.019715, rms=0.392 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64072.637 ms 0472: dt=0.000750, rms=0.392 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62725.109 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0473: dt=0.001750, rms=0.392 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59659.250 ms iter 0, gcam->neg = 26 after 22 iterations, nbhd size=2, neg = 0 0474: dt=0.064000, rms=0.392 (0.068%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61559.574 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0475: dt=0.006000, rms=0.392 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0476: dt=0.006000, rms=0.392 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0477: dt=0.006000, rms=0.392 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0478: dt=0.006000, rms=0.392 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0479: dt=0.006000, rms=0.392 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0480: dt=0.006000, rms=0.392 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0481: dt=0.006000, rms=0.392 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 15 iterations, nbhd size=2, neg = 0 0482: dt=0.006000, rms=0.391 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0483: dt=0.006000, rms=0.391 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0484: dt=0.006000, rms=0.391 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0485: dt=0.006000, rms=0.391 (0.030%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57027.777 ms iter 0, gcam->neg = 52 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28907.773 ms iter 1, dt=0.000000: new neg 5, old_neg 5, delta 0, rms=0.005 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0486: dt=11.200000, rms=0.391 (-0.300%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53155.164 ms iter 0, gcam->neg = 83 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.006, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29100.529 ms iter 1, dt=0.000000: new neg 5, old_neg 5, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0487: dt=25.600000, rms=0.391 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57472.270 ms iter 0, gcam->neg = 204 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 36491.156 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.005 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0488: dt=4.032000, rms=0.391 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70630.344 ms iter 0, gcam->neg = 301 after 200 iterations, nbhd size=2, neg = 3 starting rms=0.006, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 35677.555 ms iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0489: dt=7.760000, rms=0.391 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70943.281 ms iter 0, gcam->neg = 51 after 47 iterations, nbhd size=2, neg = 0 0490: dt=0.581081, rms=0.391 (0.246%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65967.086 ms iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0491: dt=0.112000, rms=0.391 (0.042%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 24 iterations, nbhd size=3, neg = 0 0492: dt=0.112000, rms=0.390 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 37 iterations, nbhd size=3, neg = 0 0493: dt=0.112000, rms=0.390 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 55 iterations, nbhd size=2, neg = 0 0494: dt=0.112000, rms=0.390 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 64 iterations, nbhd size=4, neg = 0 0495: dt=0.112000, rms=0.389 (0.133%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31316.021 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0496: dt=0.112000, rms=0.389 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64358.434 ms iter 0, gcam->neg = 13 after 31 iterations, nbhd size=3, neg = 0 0497: dt=0.225000, rms=0.389 (0.038%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66335.953 ms iter 0, gcam->neg = 18 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31961.701 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0498: dt=0.263158, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70471.016 ms iter 0, gcam->neg = 41 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 35261.441 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0499: dt=0.448000, rms=0.389 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61438.043 ms 0500: dt=0.000438, rms=0.388 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60809.688 ms iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0501: dt=0.016000, rms=0.388 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59885.031 ms iter 0, gcam->neg = 6 after 27 iterations, nbhd size=4, neg = 0 0502: dt=0.020000, rms=0.388 (0.085%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68260.031 ms iter 0, gcam->neg = 9 after 0 iterations, nbhd size=0, neg = 0 0503: dt=0.020000, rms=0.387 (0.082%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 37 iterations, nbhd size=1, neg = 0 0504: dt=0.020000, rms=0.387 (0.078%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 24 iterations, nbhd size=3, neg = 0 0505: dt=0.020000, rms=0.387 (0.140%), neg=0, invalid=766 iter 0, gcam->neg = 23 after 48 iterations, nbhd size=2, neg = 0 0506: dt=0.020000, rms=0.386 (0.185%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 34296.938 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0507: dt=0.020000, rms=0.386 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65599.539 ms iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0508: dt=0.007000, rms=0.386 (0.019%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66915.305 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0509: dt=0.007000, rms=0.386 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66824.797 ms iter 0, gcam->neg = 7 after 18 iterations, nbhd size=2, neg = 0 0510: dt=0.028000, rms=0.385 (0.081%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65932.648 ms iter 0, gcam->neg = 1 after 21 iterations, nbhd size=3, neg = 0 0511: dt=0.001250, rms=0.385 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.385, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66781.148 ms 0512: dt=0.001750, rms=0.385 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66682.602 ms 0513: dt=0.001250, rms=0.385 (0.006%), neg=0, invalid=766 0514: dt=0.001250, rms=0.385 (0.006%), neg=0, invalid=766 0515: dt=0.001250, rms=0.385 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 46 iterations, nbhd size=3, neg = 0 0516: dt=0.001250, rms=0.385 (0.014%), neg=0, invalid=766 0517: dt=0.001250, rms=0.385 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 61 iterations, nbhd size=2, neg = 0 0518: dt=0.001250, rms=0.385 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 25 iterations, nbhd size=4, neg = 0 0519: dt=0.001250, rms=0.385 (0.026%), neg=0, invalid=766 0520: dt=0.001250, rms=0.385 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 44 iterations, nbhd size=2, neg = 0 0521: dt=0.001250, rms=0.385 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0522: dt=0.001250, rms=0.385 (0.034%), neg=0, invalid=766 0523: dt=0.001250, rms=0.384 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 17 iterations, nbhd size=2, neg = 0 0524: dt=0.001250, rms=0.384 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 12 iterations, nbhd size=2, neg = 0 0525: dt=0.001250, rms=0.384 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 16 iterations, nbhd size=2, neg = 0 0526: dt=0.001250, rms=0.384 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 31 iterations, nbhd size=4, neg = 0 0527: dt=0.001250, rms=0.384 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 21 iterations, nbhd size=3, neg = 0 0528: dt=0.001250, rms=0.384 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0529: dt=0.001250, rms=0.384 (0.038%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63232.758 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0530: dt=0.000750, rms=0.383 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59069.266 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0531: dt=0.007000, rms=0.383 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57804.906 ms iter 0, gcam->neg = 10 after 20 iterations, nbhd size=3, neg = 0 0532: dt=0.016000, rms=0.383 (0.068%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58021.621 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0533: dt=0.007000, rms=0.383 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 15 iterations, nbhd size=2, neg = 0 0534: dt=0.007000, rms=0.383 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0535: dt=0.007000, rms=0.383 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 24 iterations, nbhd size=3, neg = 0 0536: dt=0.007000, rms=0.382 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 22 iterations, nbhd size=3, neg = 0 0537: dt=0.007000, rms=0.382 (0.088%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 25 iterations, nbhd size=3, neg = 0 0538: dt=0.007000, rms=0.382 (0.099%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 30 iterations, nbhd size=4, neg = 0 0539: dt=0.007000, rms=0.381 (0.105%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 28 iterations, nbhd size=4, neg = 0 0540: dt=0.007000, rms=0.381 (0.114%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 29 iterations, nbhd size=4, neg = 0 0541: dt=0.007000, rms=0.380 (0.123%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 32 iterations, nbhd size=4, neg = 0 0542: dt=0.007000, rms=0.380 (0.118%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 42 iterations, nbhd size=4, neg = 0 0543: dt=0.007000, rms=0.379 (0.112%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.379, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 67067.438 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0544: dt=0.005000, rms=0.379 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65162.910 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0545: dt=0.003000, rms=0.379 (0.011%), neg=0, invalid=766 0546: dt=0.003000, rms=0.379 (0.011%), neg=0, invalid=766 0547: dt=0.003000, rms=0.379 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 25 iterations, nbhd size=3, neg = 0 0548: dt=0.003000, rms=0.379 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 20 iterations, nbhd size=3, neg = 0 0549: dt=0.003000, rms=0.379 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 21 iterations, nbhd size=3, neg = 0 0550: dt=0.003000, rms=0.379 (0.043%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 37 iterations, nbhd size=1, neg = 0 0551: dt=0.003000, rms=0.379 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 14 iterations, nbhd size=2, neg = 0 0552: dt=0.003000, rms=0.378 (0.052%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 15 iterations, nbhd size=2, neg = 0 0553: dt=0.003000, rms=0.378 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 24 iterations, nbhd size=3, neg = 0 0554: dt=0.003000, rms=0.378 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 13 iterations, nbhd size=2, neg = 0 0555: dt=0.003000, rms=0.378 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 7 iterations, nbhd size=1, neg = 0 0556: dt=0.003000, rms=0.378 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 7 iterations, nbhd size=1, neg = 0 0557: dt=0.003000, rms=0.377 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 18 iterations, nbhd size=2, neg = 0 0558: dt=0.003000, rms=0.377 (0.061%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.377, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57081.633 ms 0559: dt=0.000109, rms=0.377 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55867.918 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0560: dt=0.001750, rms=0.377 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56768.684 ms iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0561: dt=0.005016, rms=0.377 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60278.012 ms 0562: dt=0.000438, rms=0.377 (0.002%), neg=0, invalid=766 0563: dt=0.000438, rms=0.377 (0.002%), neg=0, invalid=766 0564: dt=0.000438, rms=0.377 (0.003%), neg=0, invalid=766 0565: dt=0.000438, rms=0.377 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 22 iterations, nbhd size=3, neg = 0 0566: dt=0.000438, rms=0.377 (0.006%), neg=0, invalid=766 0567: dt=0.000438, rms=0.377 (0.007%), neg=0, invalid=766 0568: dt=0.000438, rms=0.377 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0569: dt=0.000438, rms=0.377 (0.009%), neg=0, invalid=766 0570: dt=0.000438, rms=0.377 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 21 iterations, nbhd size=3, neg = 0 0571: dt=0.000438, rms=0.377 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 13 iterations, nbhd size=2, neg = 0 0572: dt=0.000438, rms=0.376 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 24 iterations, nbhd size=3, neg = 0 0573: dt=0.000438, rms=0.376 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0574: dt=0.000438, rms=0.376 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0575: dt=0.000438, rms=0.376 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0576: dt=0.000438, rms=0.376 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 11 iterations, nbhd size=2, neg = 0 0577: dt=0.000438, rms=0.376 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0578: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0579: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0580: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0581: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0582: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0583: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0584: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0585: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0586: dt=0.000438, rms=0.376 (0.014%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.376, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 79931.586 ms iter 0, gcam->neg = 1 after 15 iterations, nbhd size=2, neg = 0 0587: dt=0.001750, rms=0.376 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73307.547 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0588: dt=0.001750, rms=0.376 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72526.633 ms iter 0, gcam->neg = 7 after 24 iterations, nbhd size=3, neg = 0 0589: dt=0.005000, rms=0.376 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70810.727 ms 0590: dt=0.000109, rms=0.376 (0.001%), neg=0, invalid=766 0591: dt=0.000109, rms=0.376 (0.001%), neg=0, invalid=766 0592: dt=0.000109, rms=0.376 (0.001%), neg=0, invalid=766 0593: dt=0.000109, rms=0.376 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 21 iterations, nbhd size=3, neg = 0 0594: dt=0.000109, rms=0.376 (0.000%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0595: dt=0.000109, rms=0.376 (0.002%), neg=0, invalid=766 0596: dt=0.000109, rms=0.376 (0.003%), neg=0, invalid=766 0597: dt=0.000109, rms=0.376 (0.003%), neg=0, invalid=766 0598: dt=0.000109, rms=0.376 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0599: dt=0.000109, rms=0.376 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0600: dt=0.000109, rms=0.376 (0.003%), neg=0, invalid=766 0601: dt=0.000109, rms=0.376 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0602: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 0603: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0604: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0605: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0606: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 0607: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0608: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 0609: dt=0.000109, rms=0.375 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0610: dt=0.000109, rms=0.375 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0611: dt=0.000109, rms=0.375 (0.004%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 6 hours, 50 minutes and 6 seconds. #-------------------------------------- #@# CA Reg Inv Tue Mar 22 01:42:51 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Mar 22 01:44:07 EDT 2011 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11531190 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 24 seconds. #-------------------------------------- #@# SkullLTA Tue Mar 22 01:45:33 EDT 2011 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable5/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (50, 30, 18) --> (206, 200, 226) using (102, 87, 122) as brain centroid... mean wm in atlas = 126, using box (83,66,96) --> (121, 107,147) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10288.0, old_max_log_p =-10350.7 (thresh=-10340.3) 1.066 -0.019 -0.009 -7.404; 0.018 1.252 0.092 -30.654; 0.009 -0.091 0.995 -0.867; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10288.0, old_max_log_p =-10288.0 (thresh=-10277.8) 1.066 -0.019 -0.009 -7.404; 0.018 1.252 0.092 -30.654; 0.009 -0.091 0.995 -0.867; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10277.4, old_max_log_p =-10288.0 (thresh=-10277.8) 1.066 -0.019 -0.009 -7.404; 0.018 1.299 0.096 -40.095; 0.009 -0.092 1.013 -2.797; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10276.8, old_max_log_p =-10277.4 (thresh=-10267.1) 1.086 -0.019 -0.009 -9.901; 0.018 1.277 0.062 -31.619; 0.010 -0.050 1.015 -8.013; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10267.6, old_max_log_p =-10276.8 (thresh=-10266.5) 1.087 -0.028 -0.034 -5.969; 0.027 1.272 0.061 -32.634; 0.037 -0.050 1.015 -11.310; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08674 -0.02816 -0.03417 -5.96873; 0.02651 1.27206 0.06108 -32.63366; 0.03677 -0.05011 1.01468 -11.31037; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08674 -0.02816 -0.03417 -5.96873; 0.02651 1.27206 0.06108 -32.63366; 0.03677 -0.05011 1.01468 -11.31037; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10267.6 tol 0.000010 Resulting transform: 1.087 -0.028 -0.034 -5.969; 0.027 1.272 0.061 -32.634; 0.037 -0.050 1.015 -11.310; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10267.6 (old=-10350.7) transform before final EM align: 1.087 -0.028 -0.034 -5.969; 0.027 1.272 0.061 -32.634; 0.037 -0.050 1.015 -11.310; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08674 -0.02816 -0.03417 -5.96873; 0.02651 1.27206 0.06108 -32.63366; 0.03677 -0.05011 1.01468 -11.31037; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08674 -0.02816 -0.03417 -5.96873; 0.02651 1.27206 0.06108 -32.63366; 0.03677 -0.05011 1.01468 -11.31037; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1144191.9 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) dfp_em_step_func: 008: -log(p) = 1144191.1 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) dfp_em_step_func: 009: -log(p) = 1144189.6 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) dfp_em_step_func: 010: -log(p) = 1144188.8 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) dfp_em_step_func: 011: -log(p) = 1144187.6 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... dfp_em_step_func: 012: -log(p) = 1144187.0 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) dfp_em_step_func: 013: -log(p) = 1144186.2 after pass:transform: ( 1.09, -0.03, -0.03, -5.97) ( 0.03, 1.28, 0.07, -32.63) ( 0.04, -0.05, 1.01, -11.31) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 015: -log(p) = 1144186.2 tol 0.000000 final transform: 1.088 -0.026 -0.031 -5.969; 0.033 1.277 0.069 -32.634; 0.035 -0.052 1.015 -11.310; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 23 minutes and 47 seconds. #-------------------------------------- #@# SubCort Seg Tue Mar 22 02:09:23 EDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /usr/local/freesurfer/stable5/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.15978 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (6073 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (6073 voxels, peak = 5), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.16965 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (7201 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (7201 voxels, peak = 5), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.08065 (103) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (375 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (375 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.06945 (100) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (363 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (363 voxels, peak = 98), gca=98.4 gca peak = 0.27536 (62) mri peak = 0.07596 (58) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (1266 voxels, overlap=0.696) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (1266 voxels, peak = 57), gca=57.4 gca peak = 0.32745 (63) mri peak = 0.08047 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1121 voxels, overlap=0.768) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1121 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.08146 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32770 voxels, overlap=0.653) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32770 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.08860 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (33106 voxels, overlap=0.661) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (33106 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.03470 (62) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (22036 voxels, overlap=0.806) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (22036 voxels, peak = 60), gca=59.8 gca peak = 0.08598 (64) mri peak = 0.03293 (59) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (23336 voxels, overlap=0.881) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (23336 voxels, peak = 61), gca=60.8 gca peak = 0.24164 (71) mri peak = 0.09028 (71) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1150 voxels, overlap=0.999) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1150 voxels, peak = 69), gca=69.2 gca peak = 0.18227 (75) mri peak = 0.07716 (66) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1300 voxels, overlap=0.251) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1300 voxels, peak = 64), gca=63.8 gca peak = 0.10629 (62) mri peak = 0.05588 (56) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (19815 voxels, overlap=0.971) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (19815 voxels, peak = 59), gca=58.9 gca peak = 0.11668 (59) mri peak = 0.05384 (56) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21799 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21799 voxels, peak = 56), gca=56.0 gca peak = 0.17849 (88) mri peak = 0.11531 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5017 voxels, overlap=0.814) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5017 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.12516 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4725 voxels, overlap=0.723) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4725 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.10828 (56) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (482 voxels, overlap=0.583) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (482 voxels, peak = 59), gca=59.2 gca peak = 0.42394 (62) mri peak = 0.11261 (58) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (601 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (601 voxels, peak = 57), gca=57.4 gca peak = 0.10041 (96) mri peak = 0.06672 (90) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3853 voxels, overlap=0.813) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3853 voxels, peak = 91), gca=91.2 gca peak = 0.13978 (88) mri peak = 0.06094 (88) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3709 voxels, overlap=0.951) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3709 voxels, peak = 86), gca=85.8 gca peak = 0.08514 (81) mri peak = 0.05502 (81) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2097 voxels, overlap=0.567) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2097 voxels, peak = 73), gca=72.9 gca peak = 0.09624 (82) mri peak = 0.06313 (76) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2170 voxels, overlap=0.679) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2170 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.06079 (90) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9780 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9780 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.08673 (103) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1067 voxels, overlap=0.642) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1067 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.07914 (103) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1076 voxels, overlap=0.844) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1076 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.13661 ( 6) Third_Ventricle (14): linear fit = 0.30 x + 0.0 (182 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.30 x + 0.0 (182 voxels, peak = 11), gca=10.8 gca peak = 0.26069 (23) mri peak = 0.22414 ( 8) Fourth_Ventricle (15): linear fit = 0.25 x + 0.0 (461 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.25 x + 0.0 (461 voxels, peak = 6), gca=5.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.93 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.15978 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6073 voxels, overlap=0.777) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6073 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.16965 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.65 x + 0.0 (7201 voxels, overlap=0.825) Right_Lateral_Ventricle (43): linear fit = 0.65 x + 0.0 (7201 voxels, peak = 6), gca=5.8 gca peak = 0.30362 (100) mri peak = 0.08065 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (375 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (375 voxels, peak = 100), gca=100.0 gca peak = 0.16124 (98) mri peak = 0.06945 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (363 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (363 voxels, peak = 98), gca=98.0 gca peak = 0.30584 (57) mri peak = 0.07596 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1266 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1266 voxels, peak = 57), gca=57.0 gca peak = 0.30366 (58) mri peak = 0.08047 (61) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1121 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1121 voxels, peak = 58), gca=58.0 gca peak = 0.08345 (108) mri peak = 0.08146 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32770 voxels, overlap=0.757) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32770 voxels, peak = 108), gca=108.0 gca peak = 0.08551 (108) mri peak = 0.08860 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33106 voxels, overlap=0.746) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33106 voxels, peak = 108), gca=108.0 gca peak = 0.08255 (60) mri peak = 0.03470 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22036 voxels, overlap=0.938) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22036 voxels, peak = 62), gca=61.5 gca peak = 0.09377 (61) mri peak = 0.03293 (59) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23336 voxels, overlap=0.963) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23336 voxels, peak = 63), gca=62.5 gca peak = 0.27446 (72) mri peak = 0.09028 (71) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1150 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1150 voxels, peak = 70), gca=70.2 gca peak = 0.17680 (64) mri peak = 0.07716 (66) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1300 voxels, overlap=0.994) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1300 voxels, peak = 64), gca=64.0 gca peak = 0.11076 (58) mri peak = 0.05588 (56) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19815 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19815 voxels, peak = 59), gca=59.4 gca peak = 0.12352 (57) mri peak = 0.05384 (56) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21799 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21799 voxels, peak = 57), gca=57.0 gca peak = 0.16848 (92) mri peak = 0.11531 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5017 voxels, overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5017 voxels, peak = 92), gca=92.0 gca peak = 0.15998 (91) mri peak = 0.12516 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4725 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4725 voxels, peak = 91), gca=91.0 gca peak = 0.41356 (59) mri peak = 0.10828 (56) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (482 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (482 voxels, peak = 60), gca=60.5 gca peak = 0.41685 (58) mri peak = 0.11261 (58) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (601 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (601 voxels, peak = 58), gca=58.0 gca peak = 0.10151 (91) mri peak = 0.06672 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3853 voxels, overlap=0.994) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3853 voxels, peak = 91), gca=91.0 gca peak = 0.11274 (83) mri peak = 0.06094 (88) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3709 voxels, overlap=0.995) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3709 voxels, peak = 85), gca=85.1 gca peak = 0.09324 (74) mri peak = 0.05502 (81) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2097 voxels, overlap=0.859) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2097 voxels, peak = 74), gca=74.0 gca peak = 0.11772 (70) mri peak = 0.06313 (76) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2170 voxels, overlap=0.999) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2170 voxels, peak = 68), gca=68.2 gca peak = 0.07366 (90) mri peak = 0.06079 (90) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9780 voxels, overlap=0.859) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9780 voxels, peak = 90), gca=90.0 gca peak = 0.12200 (98) mri peak = 0.08673 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1067 voxels, overlap=0.813) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1067 voxels, peak = 98), gca=98.0 gca peak = 0.13269 (99) mri peak = 0.07914 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1076 voxels, overlap=0.871) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1076 voxels, peak = 99), gca=99.0 gca peak = 0.35640 (14) mri peak = 0.13661 ( 6) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (182 voxels, overlap=0.658) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (182 voxels, peak = 11), gca=10.8 gca peak = 0.33827 ( 9) mri peak = 0.22414 ( 8) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (461 voxels, overlap=0.756) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (461 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24950 (33) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.53035 (60) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.62779 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.24679 (29) gca peak Right_Accumbens_area = 0.32731 (70) gca peak Right_vessel = 0.79692 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.14092 (84) gca peak non_WM_hypointensities = 0.11940 (54) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.66 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 14389 gm and wm labels changed (%17 to gray, %83 to white out of all changed labels) 320 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 83766 changed. image ll: -2.168, PF=1.000 pass 2: 13952 changed. image ll: -2.167, PF=1.000 pass 3: 5407 changed. pass 4: 2515 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 18 minutes and 37 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/cc_up.lta good_output_5.1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/cc_up.lta reading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/norm.mgz 6093 voxels in left wm, 15921 in right wm, xrange [125, 130] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 global minimum found at slice 127.0, rotations (-0.30, 0.49) final transformation (x=127.0, yr=-0.300, zr=0.490): 1.000 -0.009 -0.005 2.386; 0.009 1.000 -0.000 29.922; 0.005 -0.000 1.000 22.337; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 145 177 eigenvectors: 0.000 -0.008 1.000; -0.005 -1.000 -0.008; 1.000 -0.005 -0.000; writing aseg with callosum to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Tue Mar 22 02:28:41 EDT 2011 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Mar 22 02:28:43 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 2090 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 3 minutes and 36 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 109 gm peak at 62 (62), valley at 35 (35) csf peak at 10, setting threshold to 44 white matter peak found at 111 white matter peak found at 110 gm peak at 62 (62), valley at 35 (35) csf peak at 10, setting threshold to 44 #-------------------------------------------- #@# Mask BFS Tue Mar 22 02:32:22 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1504018 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Mar 22 02:32:28 EDT 2011 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 106.1 +- 5.0 [80.0 --> 125.0] GM (70.0) : 68.3 +- 10.0 [30.0 --> 96.0] setting bottom of white matter range to 78.3 setting top of gray matter range to 88.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 3307 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5798 filled 2012 bright non-wm voxels segmented. 2161 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.65 minutes reading wm segmentation from wm.seg.mgz... 189 voxels added to wm to prevent paths from MTL structures to cortex 2327 additional wm voxels added 0 additional wm voxels added SEG EDIT: 88601 voxels turned on, 27699 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 38 found - 38 modified | TOTAL: 38 pass 2 (xy+): 0 found - 38 modified | TOTAL: 38 pass 1 (xy-): 35 found - 35 modified | TOTAL: 73 pass 2 (xy-): 0 found - 35 modified | TOTAL: 73 pass 1 (yz+): 46 found - 46 modified | TOTAL: 119 pass 2 (yz+): 0 found - 46 modified | TOTAL: 119 pass 1 (yz-): 26 found - 26 modified | TOTAL: 145 pass 2 (yz-): 0 found - 26 modified | TOTAL: 145 pass 1 (xz+): 27 found - 27 modified | TOTAL: 172 pass 2 (xz+): 0 found - 27 modified | TOTAL: 172 pass 1 (xz-): 26 found - 26 modified | TOTAL: 198 pass 2 (xz-): 0 found - 26 modified | TOTAL: 198 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 10 found - 10 modified | TOTAL: 30 pass 2 (+++): 0 found - 10 modified | TOTAL: 30 pass 1 (+++): 32 found - 32 modified | TOTAL: 62 pass 2 (+++): 0 found - 32 modified | TOTAL: 62 pass 1 (+++): 10 found - 10 modified | TOTAL: 72 pass 2 (+++): 0 found - 10 modified | TOTAL: 72 Iteration Number : 1 pass 1 (++): 90 found - 90 modified | TOTAL: 90 pass 2 (++): 0 found - 90 modified | TOTAL: 90 pass 1 (+-): 103 found - 103 modified | TOTAL: 193 pass 2 (+-): 1 found - 104 modified | TOTAL: 194 pass 3 (+-): 0 found - 104 modified | TOTAL: 194 pass 1 (--): 97 found - 97 modified | TOTAL: 291 pass 2 (--): 0 found - 97 modified | TOTAL: 291 pass 1 (-+): 70 found - 70 modified | TOTAL: 361 pass 2 (-+): 0 found - 70 modified | TOTAL: 361 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 6 found - 6 modified | TOTAL: 10 pass 2 (xy-): 0 found - 6 modified | TOTAL: 10 pass 1 (yz+): 6 found - 6 modified | TOTAL: 16 pass 2 (yz+): 0 found - 6 modified | TOTAL: 16 pass 1 (yz-): 4 found - 4 modified | TOTAL: 20 pass 2 (yz-): 0 found - 4 modified | TOTAL: 20 pass 1 (xz+): 4 found - 4 modified | TOTAL: 24 pass 2 (xz+): 0 found - 4 modified | TOTAL: 24 pass 1 (xz-): 3 found - 3 modified | TOTAL: 27 pass 2 (xz-): 0 found - 3 modified | TOTAL: 27 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 2 found - 2 modified | TOTAL: 9 pass 2 (-+): 0 found - 2 modified | TOTAL: 9 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 2 found - 2 modified | TOTAL: 3 pass 2 (xz+): 0 found - 2 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 675 (out of 516592: 0.130664) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Mar 22 02:35:00 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.066 -0.019 -0.009 -7.404; 0.018 1.252 0.092 -30.654; 0.009 -0.091 0.995 -0.867; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.066 -0.019 -0.009 -7.404; 0.018 1.252 0.092 -30.654; 0.009 -0.091 0.995 -0.867; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1555 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) need search nearby using seed (124, 115, 88), TAL = (4.0, -40.0, 13.0) talairach voxel to voxel transform 0.938 0.014 0.007 7.390; -0.013 0.793 -0.074 24.161; -0.010 0.072 0.999 3.003; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 115, 88) --> (4.0, -40.0, 13.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (4.00, -40.00, 13.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -40.00, 13.00) SRC: (109.03, 107.56, 98.12) search lh wm seed point around talairach space (-14.00, -40.00, 13.00), SRC: (142.78, 107.11, 97.76) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue Mar 22 02:36:05 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 4 found - 4 modified | TOTAL: 8 pass 2 (xz+): 0 found - 4 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 1 found - 1 modified | TOTAL: 6 pass 2 (-+): 0 found - 1 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 18 (out of 248028: 0.007257) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ slice 40: 1022 vertices, 1119 faces slice 50: 5530 vertices, 5754 faces slice 60: 12133 vertices, 12350 faces slice 70: 20240 vertices, 20612 faces slice 80: 29319 vertices, 29642 faces slice 90: 38152 vertices, 38435 faces slice 100: 47564 vertices, 47947 faces slice 110: 59303 vertices, 59663 faces slice 120: 70251 vertices, 70646 faces slice 130: 80582 vertices, 80940 faces slice 140: 90470 vertices, 90844 faces slice 150: 99263 vertices, 99549 faces slice 160: 106558 vertices, 106838 faces slice 170: 113471 vertices, 113711 faces slice 180: 119494 vertices, 119680 faces slice 190: 123640 vertices, 123786 faces slice 200: 125436 vertices, 125466 faces slice 210: 125446 vertices, 125470 faces slice 220: 125446 vertices, 125470 faces slice 230: 125446 vertices, 125470 faces slice 240: 125446 vertices, 125470 faces slice 250: 125446 vertices, 125470 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 125446 voxel in cpt #1: X=-24 [v=125446,e=376410,f=250940] located at (-27.110134, -15.075961, 24.123934) For the whole surface: X=-24 [v=125446,e=376410,f=250940] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Mar 22 02:36:18 EDT 2011 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Mar 22 02:36:24 EDT 2011 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts avg radius = 46.0 mm, total surface area = 66394 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Mar 22 02:37:15 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.58 (0.00-->6.59) (max @ vno 40419 --> 41288) face area 0.03 +- 0.03 (-0.06-->0.72) scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.224, avgs=0 005/300: dt: 0.9000, rms radial error=176.964, avgs=0 010/300: dt: 0.9000, rms radial error=176.404, avgs=0 015/300: dt: 0.9000, rms radial error=175.671, avgs=0 020/300: dt: 0.9000, rms radial error=174.837, avgs=0 025/300: dt: 0.9000, rms radial error=173.945, avgs=0 030/300: dt: 0.9000, rms radial error=173.021, avgs=0 035/300: dt: 0.9000, rms radial error=172.080, avgs=0 040/300: dt: 0.9000, rms radial error=171.131, avgs=0 045/300: dt: 0.9000, rms radial error=170.180, avgs=0 050/300: dt: 0.9000, rms radial error=169.230, avgs=0 055/300: dt: 0.9000, rms radial error=168.282, avgs=0 060/300: dt: 0.9000, rms radial error=167.338, avgs=0 065/300: dt: 0.9000, rms radial error=166.398, avgs=0 070/300: dt: 0.9000, rms radial error=165.463, avgs=0 075/300: dt: 0.9000, rms radial error=164.532, avgs=0 080/300: dt: 0.9000, rms radial error=163.607, avgs=0 085/300: dt: 0.9000, rms radial error=162.686, avgs=0 090/300: dt: 0.9000, rms radial error=161.771, avgs=0 095/300: dt: 0.9000, rms radial error=160.860, avgs=0 100/300: dt: 0.9000, rms radial error=159.954, avgs=0 105/300: dt: 0.9000, rms radial error=159.053, avgs=0 110/300: dt: 0.9000, rms radial error=158.156, avgs=0 115/300: dt: 0.9000, rms radial error=157.265, avgs=0 120/300: dt: 0.9000, rms radial error=156.378, avgs=0 125/300: dt: 0.9000, rms radial error=155.497, avgs=0 130/300: dt: 0.9000, rms radial error=154.620, avgs=0 135/300: dt: 0.9000, rms radial error=153.748, avgs=0 140/300: dt: 0.9000, rms radial error=152.881, avgs=0 145/300: dt: 0.9000, rms radial error=152.019, avgs=0 150/300: dt: 0.9000, rms radial error=151.163, avgs=0 155/300: dt: 0.9000, rms radial error=150.312, avgs=0 160/300: dt: 0.9000, rms radial error=149.466, avgs=0 165/300: dt: 0.9000, rms radial error=148.625, avgs=0 170/300: dt: 0.9000, rms radial error=147.789, avgs=0 175/300: dt: 0.9000, rms radial error=146.958, avgs=0 180/300: dt: 0.9000, rms radial error=146.132, avgs=0 185/300: dt: 0.9000, rms radial error=145.310, avgs=0 190/300: dt: 0.9000, rms radial error=144.493, avgs=0 195/300: dt: 0.9000, rms radial error=143.680, avgs=0 200/300: dt: 0.9000, rms radial error=142.871, avgs=0 205/300: dt: 0.9000, rms radial error=142.067, avgs=0 210/300: dt: 0.9000, rms radial error=141.268, avgs=0 215/300: dt: 0.9000, rms radial error=140.472, avgs=0 220/300: dt: 0.9000, rms radial error=139.682, avgs=0 225/300: dt: 0.9000, rms radial error=138.895, avgs=0 230/300: dt: 0.9000, rms radial error=138.113, avgs=0 235/300: dt: 0.9000, rms radial error=137.335, avgs=0 240/300: dt: 0.9000, rms radial error=136.562, avgs=0 245/300: dt: 0.9000, rms radial error=135.793, avgs=0 250/300: dt: 0.9000, rms radial error=135.028, avgs=0 255/300: dt: 0.9000, rms radial error=134.267, avgs=0 260/300: dt: 0.9000, rms radial error=133.511, avgs=0 265/300: dt: 0.9000, rms radial error=132.759, avgs=0 270/300: dt: 0.9000, rms radial error=132.011, avgs=0 275/300: dt: 0.9000, rms radial error=131.267, avgs=0 280/300: dt: 0.9000, rms radial error=130.528, avgs=0 285/300: dt: 0.9000, rms radial error=129.792, avgs=0 290/300: dt: 0.9000, rms radial error=129.061, avgs=0 295/300: dt: 0.9000, rms radial error=128.334, avgs=0 300/300: dt: 0.9000, rms radial error=127.611, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14545.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2376.56 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 233.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/12 = 0.01053 epoch 4 (K=640.0), pass 1, starting sse = 11.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/16 = 0.00765 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Mar 22 02:43:21 EDT 2011 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 good_output_5.1 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ before topology correction, eno=-24 (nv=125446, nf=250940, ne=376410, g=13) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 2564 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 22 defects to be corrected 0 vertices coincident reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4290 (-4.7145) -vertex loglikelihood: -6.5798 (-3.2899) -normal dot loglikelihood: -3.5948 (-3.5948) -quad curv loglikelihood: -6.4291 (-3.2146) Total Loglikelihood : -26.0326 CORRECTING DEFECT 0 (vertices=40, convex hull=75) After retessellation of defect 0, euler #=-19 (123911,371198,247268) : difference with theory (-19) = 0 CORRECTING DEFECT 1 (vertices=32, convex hull=56) After retessellation of defect 1, euler #=-18 (123925,371263,247320) : difference with theory (-18) = 0 CORRECTING DEFECT 2 (vertices=211, convex hull=140) After retessellation of defect 2, euler #=-17 (123974,371473,247482) : difference with theory (-17) = 0 CORRECTING DEFECT 3 (vertices=37, convex hull=69) After retessellation of defect 3, euler #=-16 (123995,371565,247554) : difference with theory (-16) = 0 CORRECTING DEFECT 4 (vertices=67, convex hull=91) After retessellation of defect 4, euler #=-15 (124040,371738,247683) : difference with theory (-15) = 0 CORRECTING DEFECT 5 (vertices=35, convex hull=32) After retessellation of defect 5, euler #=-14 (124044,371759,247701) : difference with theory (-14) = 0 CORRECTING DEFECT 6 (vertices=160, convex hull=175) After retessellation of defect 6, euler #=-13 (124112,372040,247915) : difference with theory (-13) = 0 CORRECTING DEFECT 7 (vertices=66, convex hull=84) After retessellation of defect 7, euler #=-12 (124136,372150,248002) : difference with theory (-12) = 0 CORRECTING DEFECT 8 (vertices=23, convex hull=62) After retessellation of defect 8, euler #=-11 (124148,372210,248051) : difference with theory (-11) = 0 CORRECTING DEFECT 9 (vertices=37, convex hull=23) After retessellation of defect 9, euler #=-10 (124150,372223,248063) : difference with theory (-10) = 0 CORRECTING DEFECT 10 (vertices=9, convex hull=21) Warning - incorrect dp selected!!!!(-137.696835 >= -137.696837 ) After retessellation of defect 10, euler #=-9 (124153,372237,248075) : difference with theory (-9) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=26) After retessellation of defect 11, euler #=-8 (124160,372265,248097) : difference with theory (-8) = 0 CORRECTING DEFECT 12 (vertices=339, convex hull=55) After retessellation of defect 12, euler #=-7 (124171,372324,248146) : difference with theory (-7) = 0 CORRECTING DEFECT 13 (vertices=46, convex hull=58) After retessellation of defect 13, euler #=-6 (124193,372413,248214) : difference with theory (-6) = 0 CORRECTING DEFECT 14 (vertices=183, convex hull=59) After retessellation of defect 14, euler #=-5 (124218,372510,248287) : difference with theory (-5) = 0 CORRECTING DEFECT 15 (vertices=84, convex hull=95) After retessellation of defect 15, euler #=-4 (124243,372626,248379) : difference with theory (-4) = 0 CORRECTING DEFECT 16 (vertices=43, convex hull=70) After retessellation of defect 16, euler #=-3 (124268,372731,248460) : difference with theory (-3) = 0 CORRECTING DEFECT 17 (vertices=9, convex hull=25) After retessellation of defect 17, euler #=-2 (124269,372742,248471) : difference with theory (-2) = 0 CORRECTING DEFECT 18 (vertices=21, convex hull=29) After retessellation of defect 18, euler #=-1 (124272,372757,248484) : difference with theory (-1) = 0 CORRECTING DEFECT 19 (vertices=24, convex hull=25) After retessellation of defect 19, euler #=0 (124276,372780,248504) : difference with theory (0) = 0 CORRECTING DEFECT 20 (vertices=29, convex hull=71) After retessellation of defect 20, euler #=1 (124288,372843,248556) : difference with theory (1) = 0 CORRECTING DEFECT 21 (vertices=19, convex hull=44) After retessellation of defect 21, euler #=2 (124298,372888,248592) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.07-->7.20) (max @ vno 45854 --> 55478) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.07-->7.20) (max @ vno 45854 --> 55478) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 79 mutations (34.6%), 149 crossovers (65.4%), 38 vertices were eliminated building final representation... 1148 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=124298, nf=248592, ne=372888, g=0) writing corrected surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 14.8 minutes 0 defective edges removing intersecting faces 000: 106 intersecting 001: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 124298 - 372888 + 248592 = 2 --> 0 holes F =2V-4: 248592 = 248596-4 (0) 2E=3F: 745776 = 745776 (0) total defect index = 0 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 12 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Mar 22 02:58:17 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs good_output_5.1 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... 11083 bright wm thresholded. 2308 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.orig... computing class statistics... border white: 235150 voxels (1.40%) border gray 264987 voxels (1.58%) WM (91.0): 92.7 +- 8.9 [70.0 --> 110.0] GM (78.0) : 75.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.5 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 23.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.36) (max @ vno 124053 --> 124073) face area 0.28 +- 0.12 (0.00-->2.53) mean absolute distance = 0.86 +- 1.05 3107 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=62 using class modes intead of means.... mean inside = 91.2, mean outside = 71.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=73.3, 199 (199) missing vertices, mean dist 0.4 [0.8 (%26.6)->0.9 (%73.4))] %53 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.07-->4.20) (max @ vno 124053 --> 124073) face area 0.28 +- 0.14 (0.00-->2.10) mean absolute distance = 0.40 +- 0.72 2608 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6102951.5, rms=12.84 001: dt: 0.5000, sse=6120376.0, rms=9.62 002: dt: 0.5000, sse=6180160.0, rms=7.47 003: dt: 0.5000, sse=6349629.5, rms=5.96 004: dt: 0.5000, sse=6476752.5, rms=4.98 005: dt: 0.5000, sse=6679562.0, rms=4.40 006: dt: 0.5000, sse=6771017.5, rms=4.07 007: dt: 0.5000, sse=6892075.5, rms=3.89 008: dt: 0.5000, sse=6910179.0, rms=3.79 009: dt: 0.5000, sse=6965955.0, rms=3.72 rms = 3.69, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6948114.0, rms=3.69 011: dt: 0.2500, sse=4298524.5, rms=2.54 012: dt: 0.2500, sse=3911456.8, rms=2.23 013: dt: 0.2500, sse=3729320.8, rms=2.15 rms = 2.10, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3666470.5, rms=2.10 015: dt: 0.1250, sse=3574815.5, rms=2.03 rms = 2.03, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3549508.2, rms=2.03 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=77.0, 204 (88) missing vertices, mean dist -0.2 [0.5 (%71.1)->0.3 (%28.9))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.05-->4.21) (max @ vno 124053 --> 124073) face area 0.36 +- 0.17 (0.00-->2.81) mean absolute distance = 0.30 +- 0.45 2634 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4239096.0, rms=5.33 017: dt: 0.5000, sse=4564555.5, rms=3.39 rms = 3.57, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4187809.0, rms=2.64 019: dt: 0.2500, sse=4010275.8, rms=2.08 020: dt: 0.2500, sse=3905448.5, rms=1.80 021: dt: 0.2500, sse=3853944.2, rms=1.71 rms = 1.67, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3817624.0, rms=1.67 023: dt: 0.1250, sse=3763095.5, rms=1.61 rms = 1.61, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3739024.2, rms=1.61 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.5, 201 (74) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.08-->4.18) (max @ vno 124053 --> 124073) face area 0.35 +- 0.17 (0.00-->2.83) mean absolute distance = 0.23 +- 0.34 2701 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4138658.5, rms=4.51 025: dt: 0.5000, sse=4348716.5, rms=3.09 rms = 3.44, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4037819.5, rms=2.11 027: dt: 0.2500, sse=3945609.2, rms=1.66 028: dt: 0.2500, sse=3911776.0, rms=1.48 rms = 1.48, time step reduction 2 of 3 to 0.125... rms = 1.45, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=3881492.8, rms=1.45 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.8, 194 (68) missing vertices, mean dist -0.1 [0.3 (%58.5)->0.2 (%41.5))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3924697.0, rms=2.10 rms = 2.35, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3966638.2, rms=1.45 031: dt: 0.2500, sse=4134581.5, rms=1.09 rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.08, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4131213.0, rms=1.08 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 16 non-cortical segments detected only using segment with 1858 vertices erasing segment 1 (vno[0] = 60520) erasing segment 2 (vno[0] = 62883) erasing segment 3 (vno[0] = 66216) erasing segment 4 (vno[0] = 77448) erasing segment 5 (vno[0] = 83239) erasing segment 6 (vno[0] = 89386) erasing segment 7 (vno[0] = 93996) erasing segment 8 (vno[0] = 95552) erasing segment 9 (vno[0] = 96310) erasing segment 10 (vno[0] = 97879) erasing segment 11 (vno[0] = 98589) erasing segment 12 (vno[0] = 98592) erasing segment 13 (vno[0] = 99231) erasing segment 14 (vno[0] = 124178) erasing segment 15 (vno[0] = 124185) writing cortex label to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/lh.cortex.label... LabelWrite: saving to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/lh.cortex.label writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.area vertex spacing 0.90 +- 0.26 (0.06-->4.14) (max @ vno 124053 --> 124073) face area 0.34 +- 0.17 (0.00-->2.74) refinement took 5.7 minutes #-------------------------------------------- #@# Smooth2 lh Tue Mar 22 03:04:00 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Mar 22 03:04:06 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.1 mm, total surface area = 77542 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.020 (target=0.015) step 050: RMS=0.018 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 0.8 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 296 vertices thresholded to be in k1 ~ [-0.78 0.40], k2 ~ [-0.10 0.07] total integrated curvature = 0.553*4pi (6.951) --> 0 handles ICI = 1.4, FI = 8.4, variation=146.698 174 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 130 vertices thresholded to be in [-0.36 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Tue Mar 22 03:06:21 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm good_output_5.1 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ good_output_5.1/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 271 ] Gb_filter = 0 WARN: S lookup min: -0.020225 WARN: S explicit min: 0.000000 vertex = 415 #-------------------------------------------- #@# Sphere lh Tue Mar 22 03:06:28 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 0.86 hours scaling brain by 0.294... pass 1: epoch 1 of 3 starting distance error %19.10 pass 1: epoch 2 of 3 starting distance error %19.06 unfolding complete - removing small folds... starting distance error %19.03 removing remaining folds... final distance error %19.05 #-------------------------------------------- #@# Surf Reg lh Tue Mar 22 03:57:52 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable5/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/stable5/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.594 curvature mean = 0.034, std = 0.936 curvature mean = 0.020, std = 0.873 curvature mean = 0.024, std = 0.970 curvature mean = 0.009, std = 0.946 curvature mean = 0.024, std = 0.983 curvature mean = 0.004, std = 0.975 curvature mean = 0.023, std = 0.986 curvature mean = 0.001, std = 0.989 curvature mean = -0.026, std = 0.289 curvature mean = 0.004, std = 0.068 curvature mean = 0.065, std = 0.349 curvature mean = 0.004, std = 0.080 curvature mean = 0.030, std = 0.543 curvature mean = 0.004, std = 0.086 curvature mean = 0.016, std = 0.679 curvature mean = 0.004, std = 0.089 curvature mean = 0.006, std = 0.787 #-------------------------------------------- #@# Jacobian white lh Tue Mar 22 04:35:23 EDT 2011 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Mar 22 04:35:27 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Mar 22 04:35:30 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output_5.1 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading atlas from /usr/local/freesurfer/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1168 labels changed using aseg relabeling using gibbs priors... 000: 2772 changed, 124298 examined... 001: 662 changed, 11915 examined... 002: 161 changed, 3617 examined... 003: 54 changed, 960 examined... 004: 24 changed, 321 examined... 005: 13 changed, 140 examined... 006: 1 changed, 81 examined... 007: 0 changed, 5 examined... 237 labels changed using aseg 000: 108 total segments, 66 labels (252 vertices) changed 001: 43 total segments, 1 labels (4 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1817 vertices marked for relabeling... 1817 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 57 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Mar 22 04:36:29 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs good_output_5.1 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... 11083 bright wm thresholded. 2308 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.orig... computing class statistics... border white: 235150 voxels (1.40%) border gray 264987 voxels (1.58%) WM (91.0): 92.7 +- 8.9 [70.0 --> 110.0] GM (78.0) : 75.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.5 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 23.8 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=62 using class modes intead of means.... mean inside = 91.2, mean outside = 71.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.36) (max @ vno 124053 --> 124073) face area 0.28 +- 0.12 (0.00-->2.53) mean absolute distance = 0.86 +- 1.06 3170 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 302 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=73.3, 199 (199) missing vertices, mean dist 0.4 [0.8 (%26.6)->0.9 (%73.4))] %53 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.07-->4.20) (max @ vno 124053 --> 124073) face area 0.28 +- 0.14 (0.00-->2.10) mean absolute distance = 0.40 +- 0.72 2476 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6112289.5, rms=12.83 001: dt: 0.5000, sse=6134627.0, rms=9.62 002: dt: 0.5000, sse=6194602.5, rms=7.47 003: dt: 0.5000, sse=6363571.0, rms=5.96 004: dt: 0.5000, sse=6491750.0, rms=4.98 005: dt: 0.5000, sse=6695603.5, rms=4.40 006: dt: 0.5000, sse=6786465.0, rms=4.07 007: dt: 0.5000, sse=6910134.5, rms=3.89 008: dt: 0.5000, sse=6926802.0, rms=3.79 009: dt: 0.5000, sse=6986746.5, rms=3.72 rms = 3.69, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6965964.0, rms=3.69 011: dt: 0.2500, sse=4311502.5, rms=2.54 012: dt: 0.2500, sse=3923410.2, rms=2.23 013: dt: 0.2500, sse=3740979.0, rms=2.15 rms = 2.10, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3678572.0, rms=2.10 015: dt: 0.1250, sse=3586556.0, rms=2.04 rms = 2.03, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3561285.8, rms=2.03 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 228 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 8 with 12 points - only 50.00% unknown deleting segment 9 with 26 points - only 0.00% unknown mean border=77.0, 204 (88) missing vertices, mean dist -0.3 [0.5 (%71.1)->0.3 (%28.9))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.05-->4.21) (max @ vno 124053 --> 124073) face area 0.36 +- 0.17 (0.00-->2.81) mean absolute distance = 0.30 +- 0.45 2667 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4258820.0, rms=5.33 017: dt: 0.5000, sse=4586911.0, rms=3.40 rms = 3.58, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4209560.5, rms=2.65 019: dt: 0.2500, sse=4032916.2, rms=2.09 020: dt: 0.2500, sse=3928394.5, rms=1.82 021: dt: 0.2500, sse=3876586.0, rms=1.73 rms = 1.68, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3839515.5, rms=1.68 023: dt: 0.1250, sse=3784234.5, rms=1.63 rms = 1.62, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3759998.2, rms=1.62 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 238 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=80.5, 209 (74) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.09-->4.16) (max @ vno 124053 --> 124073) face area 0.35 +- 0.17 (0.00-->2.83) mean absolute distance = 0.23 +- 0.34 2580 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4157956.0, rms=4.51 025: dt: 0.5000, sse=4365364.0, rms=3.09 rms = 3.44, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4054230.8, rms=2.11 027: dt: 0.2500, sse=3962104.0, rms=1.67 028: dt: 0.2500, sse=3928675.5, rms=1.49 rms = 1.49, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3912867.5, rms=1.49 030: dt: 0.1250, sse=3854087.8, rms=1.42 rms = 1.42, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3854087.8, rms=1.42 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 280 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=81.8, 193 (69) missing vertices, mean dist -0.1 [0.2 (%59.5)->0.2 (%40.5))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3898435.0, rms=2.11 rms = 2.35, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3975194.0, rms=1.44 033: dt: 0.2500, sse=4155172.5, rms=1.07 rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4152015.8, rms=1.06 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=51.9, 165 (165) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.1 (%100.0))] %23 local maxima, %60 large gradients and %12 min vals, 950 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=23089936.0, rms=29.58 001: dt: 0.5000, sse=17139222.0, rms=24.93 002: dt: 0.5000, sse=12814174.0, rms=20.94 003: dt: 0.5000, sse=9873583.0, rms=17.66 004: dt: 0.5000, sse=8212400.5, rms=14.99 005: dt: 0.5000, sse=7247002.5, rms=12.78 006: dt: 0.5000, sse=6644132.0, rms=10.95 007: dt: 0.5000, sse=6202136.5, rms=9.40 008: dt: 0.5000, sse=5949834.0, rms=8.02 009: dt: 0.5000, sse=5825412.0, rms=6.87 010: dt: 0.5000, sse=5767804.0, rms=5.93 011: dt: 0.5000, sse=5820852.5, rms=5.25 012: dt: 0.5000, sse=5859520.0, rms=4.77 013: dt: 0.5000, sse=5950821.0, rms=4.45 014: dt: 0.5000, sse=5978465.0, rms=4.23 015: dt: 0.5000, sse=6047577.5, rms=4.08 016: dt: 0.5000, sse=6042246.5, rms=3.97 017: dt: 0.5000, sse=6092666.5, rms=3.89 018: dt: 0.5000, sse=6054222.5, rms=3.84 rms = 3.80, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6084595.5, rms=3.80 020: dt: 0.2500, sse=4029009.5, rms=2.95 021: dt: 0.2500, sse=3807045.5, rms=2.72 rms = 2.69, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3693451.5, rms=2.69 023: dt: 0.1250, sse=3550736.0, rms=2.57 rms = 2.56, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3532036.8, rms=2.56 positioning took 2.6 minutes mean border=48.7, 395 (39) missing vertices, mean dist 0.2 [0.2 (%44.5)->0.6 (%55.5))] %48 local maxima, %40 large gradients and % 7 min vals, 335 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4322762.0, rms=5.64 025: dt: 0.5000, sse=4455843.5, rms=4.15 026: dt: 0.5000, sse=5558272.0, rms=3.97 rms = 4.03, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4560494.0, rms=3.19 028: dt: 0.2500, sse=4218639.5, rms=2.86 029: dt: 0.2500, sse=4148630.0, rms=2.77 rms = 2.74, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4133599.0, rms=2.74 031: dt: 0.1250, sse=4011537.0, rms=2.62 rms = 2.60, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4005896.5, rms=2.60 positioning took 0.9 minutes mean border=46.0, 512 (33) missing vertices, mean dist 0.2 [0.2 (%36.8)->0.4 (%63.2))] %66 local maxima, %22 large gradients and % 7 min vals, 377 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4321157.5, rms=4.35 033: dt: 0.5000, sse=4434171.5, rms=3.85 rms = 3.89, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4159234.2, rms=3.02 035: dt: 0.2500, sse=4269570.0, rms=2.70 036: dt: 0.2500, sse=4248250.0, rms=2.63 rms = 2.61, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4270135.5, rms=2.61 038: dt: 0.1250, sse=4155650.8, rms=2.48 rms = 2.47, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4145323.8, rms=2.47 positioning took 0.7 minutes mean border=44.6, 989 (19) missing vertices, mean dist 0.1 [0.2 (%43.3)->0.3 (%56.7))] %72 local maxima, %15 large gradients and % 7 min vals, 321 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4214985.5, rms=3.00 rms = 3.56, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4088750.8, rms=2.61 041: dt: 0.2500, sse=4155029.5, rms=2.46 042: dt: 0.2500, sse=4237168.5, rms=2.40 rms = 2.37, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=4285679.0, rms=2.37 044: dt: 0.1250, sse=4192669.8, rms=2.27 rms = 2.24, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4190624.5, rms=2.24 positioning took 0.7 minutes writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.area.pial vertex spacing 1.02 +- 0.42 (0.07-->7.13) (max @ vno 84194 --> 83273) face area 0.41 +- 0.30 (0.00-->9.54) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 124298 vertices processed 25000 of 124298 vertices processed 50000 of 124298 vertices processed 75000 of 124298 vertices processed 100000 of 124298 vertices processed 0 of 124298 vertices processed 25000 of 124298 vertices processed 50000 of 124298 vertices processed 75000 of 124298 vertices processed 100000 of 124298 vertices processed thickness calculation complete, 530:621 truncations. 52711 vertices at 0 distance 81447 vertices at 1 distance 65770 vertices at 2 distance 23678 vertices at 3 distance 7236 vertices at 4 distance 2460 vertices at 5 distance 1008 vertices at 6 distance 482 vertices at 7 distance 266 vertices at 8 distance 175 vertices at 9 distance 120 vertices at 10 distance 95 vertices at 11 distance 66 vertices at 12 distance 41 vertices at 13 distance 39 vertices at 14 distance 27 vertices at 15 distance 20 vertices at 16 distance 8 vertices at 17 distance 4 vertices at 18 distance 9 vertices at 19 distance 16 vertices at 20 distance writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.thickness positioning took 12.0 minutes #-------------------------------------------- #@# Surf Volume lh Tue Mar 22 04:48:27 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Tue Mar 22 04:48:30 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab good_output_5.1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1679 1180 2794 2.359 0.462 0.112 0.029 13 2.0 bankssts 922 606 1495 2.445 0.658 0.146 0.038 18 1.4 caudalanteriorcingulate 3026 2042 5501 2.481 0.511 0.142 0.069 126 6.1 caudalmiddlefrontal 1780 1186 2224 1.674 0.411 0.153 0.057 27 4.1 cuneus 574 405 1962 3.376 0.758 0.143 0.043 7 1.1 entorhinal 4375 3048 8383 2.400 0.681 0.146 0.055 72 9.6 fusiform 6228 4284 11083 2.340 0.522 0.145 0.087 241 15.1 inferiorparietal 4737 3338 10613 2.742 0.721 0.175 0.085 122 15.0 inferiortemporal 1299 875 2387 2.498 0.871 0.154 0.059 25 2.8 isthmuscingulate 5565 3785 8737 2.065 0.550 0.154 0.054 91 12.5 lateraloccipital 3056 2138 5962 2.417 0.636 0.162 0.066 60 8.4 lateralorbitofrontal 3863 2753 5438 1.847 0.565 0.154 0.066 79 8.3 lingual 3064 2137 5513 2.238 0.812 0.166 0.185 374 12.3 medialorbitofrontal 4525 3181 10124 2.681 0.613 0.160 0.072 96 10.5 middletemporal 1165 764 1739 1.926 0.638 0.098 0.028 10 1.3 parahippocampal 1969 1279 3369 2.319 0.538 0.135 0.074 49 5.3 paracentral 2205 1496 3969 2.352 0.443 0.137 0.044 31 3.8 parsopercularis 839 548 1671 2.401 0.538 0.146 0.059 17 2.0 parsorbitalis 1673 1164 3131 2.352 0.507 0.143 0.048 24 3.1 parstriangularis 1349 910 1252 1.452 0.309 0.137 0.053 21 2.7 pericalcarine 6027 4040 8882 1.981 0.600 0.134 0.044 93 11.3 postcentral 1551 1104 2917 2.411 0.703 0.184 0.181 255 6.5 posteriorcingulate 6764 4428 12076 2.507 0.471 0.122 0.044 70 12.0 precentral 5247 3646 9565 2.402 0.621 0.159 0.103 650 28.5 precuneus 1239 822 2459 2.550 0.616 0.158 0.064 25 3.3 rostralanteriorcingulate 6750 4708 12722 2.288 0.558 0.164 0.074 143 20.9 rostralmiddlefrontal 8650 6152 18327 2.563 0.627 0.151 0.096 407 45.4 superiorfrontal 7893 5358 12701 2.144 0.546 0.144 0.055 119 18.5 superiorparietal 6304 4208 11565 2.386 0.624 0.132 0.048 90 12.9 superiortemporal 6184 4256 11666 2.416 0.535 0.163 0.081 176 23.5 supramarginal 284 214 841 2.789 0.558 0.198 0.089 10 0.9 frontalpole 678 476 2191 3.275 0.678 0.143 0.050 8 1.4 temporalpole 658 403 1162 2.503 0.452 0.140 0.050 9 1.3 transversetemporal 3612 2365 6580 2.651 0.856 0.126 0.066 227 9.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Mar 22 04:48:48 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output_5.1 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading atlas from /usr/local/freesurfer/stable5/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 39 labels changed using aseg relabeling using gibbs priors... 000: 8814 changed, 124298 examined... 001: 2174 changed, 33757 examined... 002: 647 changed, 10829 examined... 003: 297 changed, 3608 examined... 004: 149 changed, 1677 examined... 005: 58 changed, 818 examined... 006: 25 changed, 318 examined... 007: 13 changed, 124 examined... 008: 1 changed, 61 examined... 009: 2 changed, 9 examined... 010: 1 changed, 9 examined... 011: 1 changed, 5 examined... 012: 0 changed, 9 examined... 3 labels changed using aseg 000: 286 total segments, 204 labels (2423 vertices) changed 001: 102 total segments, 20 labels (110 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 122 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1135 vertices marked for relabeling... 1135 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 59 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Mar 22 04:49:49 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab good_output_5.1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1281 889 2362 2.269 0.623 0.169 0.067 28 3.6 G_and_S_frontomargin 1299 882 2267 2.171 0.695 0.146 0.046 20 2.3 G_and_S_occipital_inf 1480 956 2652 2.291 0.519 0.139 0.059 20 3.5 G_and_S_paracentral 1525 1013 3201 2.628 0.522 0.150 0.048 24 3.1 G_and_S_subcentral 680 504 1603 2.411 0.646 0.197 0.098 22 2.3 G_and_S_transv_frontopol 2525 1699 4558 2.390 0.585 0.146 0.054 42 5.6 G_and_S_cingul-Ant 1080 752 1968 2.393 0.585 0.132 0.044 14 2.1 G_and_S_cingul-Mid-Ant 1148 827 2142 2.409 0.532 0.146 0.063 21 2.5 G_and_S_cingul-Mid-Post 503 348 1339 2.975 0.657 0.199 0.103 17 1.8 G_cingul-Post-dorsal 268 168 407 2.324 0.939 0.142 0.066 5 0.5 G_cingul-Post-ventral 1510 1027 2140 1.735 0.394 0.168 0.071 35 4.2 G_cuneus 1201 804 2592 2.500 0.433 0.145 0.053 19 2.6 G_front_inf-Opercular 319 191 708 2.788 0.521 0.161 0.078 9 1.0 G_front_inf-Orbital 1173 828 2588 2.479 0.471 0.167 0.061 25 2.7 G_front_inf-Triangul 3494 2426 7777 2.522 0.554 0.177 0.107 174 14.2 G_front_middle 5967 4242 14047 2.705 0.598 0.166 0.128 408 41.9 G_front_sup 517 318 1092 2.746 0.703 0.118 0.047 7 1.0 G_Ins_lg_and_S_cent_ins 678 439 1894 3.179 0.850 0.160 0.078 15 2.1 G_insular_short 1615 1124 3485 2.481 0.469 0.168 0.161 167 4.0 G_occipital_middle 1659 1117 2423 1.940 0.477 0.165 0.056 28 3.7 G_occipital_sup 1770 1179 3898 2.573 0.670 0.151 0.058 35 4.5 G_oc-temp_lat-fusifor 2573 1776 3754 1.820 0.588 0.160 0.079 59 6.1 G_oc-temp_med-Lingual 1250 810 2888 2.664 0.985 0.120 0.077 197 4.8 G_oc-temp_med-Parahip 2109 1470 4784 2.470 0.632 0.179 0.080 56 7.1 G_orbital 1926 1303 4166 2.494 0.575 0.171 0.083 48 6.3 G_pariet_inf-Angular 3509 2413 7275 2.463 0.554 0.173 0.096 120 16.3 G_pariet_inf-Supramar 3043 2080 5997 2.381 0.501 0.158 0.073 59 9.8 G_parietal_sup 2241 1465 3520 1.995 0.489 0.144 0.055 53 5.3 G_postcentral 2442 1552 5352 2.700 0.429 0.139 0.057 34 5.7 G_precentral 2592 1816 5841 2.566 0.598 0.187 0.165 623 24.2 G_precuneus 1038 787 2409 2.384 0.701 0.196 0.208 105 4.9 G_rectus 584 373 1011 2.684 0.859 0.198 0.336 238 3.9 G_subcallosal 550 323 1011 2.479 0.413 0.133 0.052 7 1.2 G_temp_sup-G_T_transv 2441 1627 5061 2.413 0.682 0.143 0.058 43 6.2 G_temp_sup-Lateral 690 464 1516 2.832 0.772 0.121 0.078 11 1.6 G_temp_sup-Plan_polar 1089 783 2090 2.385 0.486 0.146 0.071 32 3.7 G_temp_sup-Plan_tempo 2918 2097 7612 2.860 0.733 0.195 0.103 92 11.2 G_temporal_inf 3021 2163 7534 2.800 0.594 0.181 0.091 85 8.8 G_temporal_middle 299 200 388 2.017 0.402 0.103 0.021 2 0.3 Lat_Fis-ant-Horizont 278 199 365 2.033 0.376 0.122 0.027 2 0.3 Lat_Fis-ant-Vertical 1284 862 1634 2.249 0.498 0.126 0.039 12 1.9 Lat_Fis-post 1795 1215 2485 1.807 0.510 0.157 0.060 31 4.8 Pole_occipital 1727 1211 4928 3.033 0.736 0.156 0.056 28 4.0 Pole_temporal 1523 1062 1742 1.721 0.663 0.135 0.047 20 2.6 S_calcarine 3048 2064 3519 1.925 0.595 0.107 0.034 20 4.0 S_central 1046 732 1506 2.095 0.567 0.113 0.029 7 1.4 S_cingul-Marginalis 506 338 834 2.597 0.529 0.112 0.040 3 0.7 S_circular_insula_ant 1599 1055 2103 2.171 0.694 0.098 0.029 11 1.9 S_circular_insula_inf 1617 1075 2196 2.319 0.468 0.116 0.035 12 2.4 S_circular_insula_sup 827 578 1575 2.604 0.712 0.138 0.048 12 1.6 S_collat_transv_ant 356 255 405 1.843 0.387 0.134 0.033 3 0.5 S_collat_transv_post 1908 1291 3050 2.271 0.485 0.137 0.041 25 3.2 S_front_inf 901 643 1556 2.137 0.565 0.142 0.058 12 1.6 S_front_middle 2517 1749 3895 2.247 0.550 0.120 0.040 21 3.9 S_front_sup 424 293 729 2.499 0.637 0.167 0.075 6 1.2 S_interm_prim-Jensen 2338 1588 3058 2.065 0.562 0.126 0.039 27 3.6 S_intrapariet_and_P_trans 537 366 716 2.121 0.485 0.155 0.045 7 0.9 S_oc_middle_and_Lunatus 1314 878 1693 2.082 0.490 0.110 0.032 9 1.7 S_oc_sup_and_transversal 673 451 870 2.041 0.388 0.114 0.029 5 0.8 S_occipital_ant 711 495 1148 2.301 0.545 0.152 0.061 15 1.4 S_oc-temp_lat 2337 1731 3141 1.939 0.523 0.134 0.045 33 4.1 S_oc-temp_med_and_Lingual 383 258 581 2.169 0.407 0.127 0.047 4 0.6 S_orbital_lateral 854 592 1191 1.915 0.875 0.114 0.129 17 2.0 S_orbital_med-olfact 936 654 1594 2.307 0.620 0.151 0.055 12 2.2 S_orbital-H_Shaped 1813 1233 2372 2.126 0.684 0.143 0.048 22 3.8 S_parieto_occipital 1259 799 1529 2.356 0.893 0.167 0.181 245 4.6 S_pericallosal 3271 2183 4454 2.073 0.509 0.134 0.040 35 5.5 S_postcentral 1634 1116 2505 2.348 0.415 0.112 0.031 12 2.2 S_precentral-inf-part 749 543 1058 2.280 0.385 0.103 0.020 3 0.7 S_precentral-sup-part 672 452 1057 2.217 0.744 0.158 0.064 13 1.6 S_suborbital 1175 803 1821 2.214 0.490 0.131 0.036 11 1.7 S_subparietal 1197 829 1911 2.456 0.594 0.130 0.049 15 1.9 S_temporal_inf 6201 4267 9939 2.308 0.490 0.123 0.044 71 10.7 S_temporal_sup 317 201 488 2.652 0.511 0.144 0.042 4 0.6 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Tue Mar 22 04:50:07 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 254738: 0.003140) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ slice 40: 643 vertices, 704 faces slice 50: 4534 vertices, 4747 faces slice 60: 10864 vertices, 11086 faces slice 70: 18373 vertices, 18697 faces slice 80: 27242 vertices, 27537 faces slice 90: 35956 vertices, 36276 faces slice 100: 45385 vertices, 45753 faces slice 110: 56328 vertices, 56691 faces slice 120: 66964 vertices, 67368 faces slice 130: 77369 vertices, 77729 faces slice 140: 87161 vertices, 87548 faces slice 150: 96894 vertices, 97236 faces slice 160: 104507 vertices, 104812 faces slice 170: 111977 vertices, 112253 faces slice 180: 118574 vertices, 118783 faces slice 190: 123787 vertices, 123977 faces slice 200: 126720 vertices, 126786 faces slice 210: 126848 vertices, 126886 faces slice 220: 126848 vertices, 126886 faces slice 230: 126848 vertices, 126886 faces slice 240: 126848 vertices, 126886 faces slice 250: 126848 vertices, 126886 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 126848 voxel in cpt #1: X=-38 [v=126848,e=380658,f=253772] located at (27.568783, -11.728880, 24.431595) For the whole surface: X=-38 [v=126848,e=380658,f=253772] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Mar 22 04:50:20 EDT 2011 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Tue Mar 22 04:50:26 EDT 2011 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts avg radius = 46.8 mm, total surface area = 67435 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Mar 22 04:51:13 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.57 (0.00-->5.74) (max @ vno 43977 --> 44004) face area 0.03 +- 0.03 (-0.06-->0.53) scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.047, avgs=0 005/300: dt: 0.9000, rms radial error=176.787, avgs=0 010/300: dt: 0.9000, rms radial error=176.229, avgs=0 015/300: dt: 0.9000, rms radial error=175.494, avgs=0 020/300: dt: 0.9000, rms radial error=174.658, avgs=0 025/300: dt: 0.9000, rms radial error=173.762, avgs=0 030/300: dt: 0.9000, rms radial error=172.837, avgs=0 035/300: dt: 0.9000, rms radial error=171.900, avgs=0 040/300: dt: 0.9000, rms radial error=170.956, avgs=0 045/300: dt: 0.9000, rms radial error=170.009, avgs=0 050/300: dt: 0.9000, rms radial error=169.062, avgs=0 055/300: dt: 0.9000, rms radial error=168.118, avgs=0 060/300: dt: 0.9000, rms radial error=167.178, avgs=0 065/300: dt: 0.9000, rms radial error=166.242, avgs=0 070/300: dt: 0.9000, rms radial error=165.310, avgs=0 075/300: dt: 0.9000, rms radial error=164.383, avgs=0 080/300: dt: 0.9000, rms radial error=163.461, avgs=0 085/300: dt: 0.9000, rms radial error=162.544, avgs=0 090/300: dt: 0.9000, rms radial error=161.632, avgs=0 095/300: dt: 0.9000, rms radial error=160.725, avgs=0 100/300: dt: 0.9000, rms radial error=159.823, avgs=0 105/300: dt: 0.9000, rms radial error=158.926, avgs=0 110/300: dt: 0.9000, rms radial error=158.034, avgs=0 115/300: dt: 0.9000, rms radial error=157.147, avgs=0 120/300: dt: 0.9000, rms radial error=156.265, avgs=0 125/300: dt: 0.9000, rms radial error=155.387, avgs=0 130/300: dt: 0.9000, rms radial error=154.515, avgs=0 135/300: dt: 0.9000, rms radial error=153.647, avgs=0 140/300: dt: 0.9000, rms radial error=152.784, avgs=0 145/300: dt: 0.9000, rms radial error=151.926, avgs=0 150/300: dt: 0.9000, rms radial error=151.072, avgs=0 155/300: dt: 0.9000, rms radial error=150.223, avgs=0 160/300: dt: 0.9000, rms radial error=149.378, avgs=0 165/300: dt: 0.9000, rms radial error=148.538, avgs=0 170/300: dt: 0.9000, rms radial error=147.703, avgs=0 175/300: dt: 0.9000, rms radial error=146.873, avgs=0 180/300: dt: 0.9000, rms radial error=146.046, avgs=0 185/300: dt: 0.9000, rms radial error=145.225, avgs=0 190/300: dt: 0.9000, rms radial error=144.408, avgs=0 195/300: dt: 0.9000, rms radial error=143.595, avgs=0 200/300: dt: 0.9000, rms radial error=142.787, avgs=0 205/300: dt: 0.9000, rms radial error=141.983, avgs=0 210/300: dt: 0.9000, rms radial error=141.184, avgs=0 215/300: dt: 0.9000, rms radial error=140.389, avgs=0 220/300: dt: 0.9000, rms radial error=139.598, avgs=0 225/300: dt: 0.9000, rms radial error=138.812, avgs=0 230/300: dt: 0.9000, rms radial error=138.030, avgs=0 235/300: dt: 0.9000, rms radial error=137.253, avgs=0 240/300: dt: 0.9000, rms radial error=136.479, avgs=0 245/300: dt: 0.9000, rms radial error=135.710, avgs=0 250/300: dt: 0.9000, rms radial error=134.946, avgs=0 255/300: dt: 0.9000, rms radial error=134.185, avgs=0 260/300: dt: 0.9000, rms radial error=133.429, avgs=0 265/300: dt: 0.9000, rms radial error=132.677, avgs=0 270/300: dt: 0.9000, rms radial error=131.930, avgs=0 275/300: dt: 0.9000, rms radial error=131.186, avgs=0 280/300: dt: 0.9000, rms radial error=130.447, avgs=0 285/300: dt: 0.9000, rms radial error=129.712, avgs=0 290/300: dt: 0.9000, rms radial error=128.980, avgs=0 295/300: dt: 0.9000, rms radial error=128.253, avgs=0 300/300: dt: 0.9000, rms radial error=127.530, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14728.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2408.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 3 (K=160.0), pass 1, starting sse = 238.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/14 = 0.00997 epoch 4 (K=640.0), pass 1, starting sse = 12.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.26/21 = 0.01219 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Mar 22 04:57:21 EDT 2011 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 good_output_5.1 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ before topology correction, eno=-38 (nv=126848, nf=253772, ne=380658, g=20) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 2671 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 25 defects to be corrected 0 vertices coincident reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4483 (-4.7241) -vertex loglikelihood: -6.4734 (-3.2367) -normal dot loglikelihood: -3.5764 (-3.5764) -quad curv loglikelihood: -6.3689 (-3.1845) Total Loglikelihood : -25.8670 CORRECTING DEFECT 0 (vertices=31, convex hull=64) After retessellation of defect 0, euler #=-22 (125232,375081,249827) : difference with theory (-22) = 0 CORRECTING DEFECT 1 (vertices=29, convex hull=62) After retessellation of defect 1, euler #=-21 (125249,375155,249885) : difference with theory (-21) = 0 CORRECTING DEFECT 2 (vertices=36, convex hull=89) After retessellation of defect 2, euler #=-20 (125268,375247,249959) : difference with theory (-20) = 0 CORRECTING DEFECT 3 (vertices=31, convex hull=50) After retessellation of defect 3, euler #=-19 (125277,375293,249997) : difference with theory (-19) = 0 CORRECTING DEFECT 4 (vertices=42, convex hull=28) After retessellation of defect 4, euler #=-18 (125281,375313,250014) : difference with theory (-18) = 0 CORRECTING DEFECT 5 (vertices=39, convex hull=70) After retessellation of defect 5, euler #=-17 (125301,375401,250083) : difference with theory (-17) = 0 CORRECTING DEFECT 6 (vertices=38, convex hull=82) After retessellation of defect 6, euler #=-16 (125326,375512,250170) : difference with theory (-16) = 0 CORRECTING DEFECT 7 (vertices=18, convex hull=48) After retessellation of defect 7, euler #=-15 (125335,375558,250208) : difference with theory (-15) = 0 CORRECTING DEFECT 8 (vertices=41, convex hull=82) After retessellation of defect 8, euler #=-14 (125359,375664,250291) : difference with theory (-14) = 0 CORRECTING DEFECT 9 (vertices=8, convex hull=14) After retessellation of defect 9, euler #=-13 (125360,375669,250296) : difference with theory (-13) = 0 CORRECTING DEFECT 10 (vertices=43, convex hull=80) After retessellation of defect 10, euler #=-12 (125386,375784,250386) : difference with theory (-12) = 0 CORRECTING DEFECT 11 (vertices=72, convex hull=42) After retessellation of defect 11, euler #=-11 (125392,375817,250414) : difference with theory (-11) = 0 CORRECTING DEFECT 12 (vertices=27, convex hull=28) After retessellation of defect 12, euler #=-10 (125394,375834,250430) : difference with theory (-10) = 0 CORRECTING DEFECT 13 (vertices=23, convex hull=35) After retessellation of defect 13, euler #=-9 (125395,375854,250450) : difference with theory (-9) = 0 CORRECTING DEFECT 14 (vertices=96, convex hull=33) After retessellation of defect 14, euler #=-8 (125401,375880,250471) : difference with theory (-8) = 0 CORRECTING DEFECT 15 (vertices=128, convex hull=119) After retessellation of defect 15, euler #=-7 (125454,376090,250629) : difference with theory (-7) = 0 CORRECTING DEFECT 16 (vertices=40, convex hull=17) After retessellation of defect 16, euler #=-6 (125456,376100,250638) : difference with theory (-6) = 0 CORRECTING DEFECT 17 (vertices=476, convex hull=97) After retessellation of defect 17, euler #=-5 (125467,376177,250705) : difference with theory (-5) = 0 CORRECTING DEFECT 18 (vertices=9, convex hull=21) Warning - incorrect dp selected!!!!(-78.627359 >= -78.627365 ) After retessellation of defect 18, euler #=-4 (125469,376191,250718) : difference with theory (-4) = 0 CORRECTING DEFECT 19 (vertices=100, convex hull=147) After retessellation of defect 19, euler #=-3 (125518,376414,250893) : difference with theory (-3) = 0 CORRECTING DEFECT 20 (vertices=72, convex hull=32) After retessellation of defect 20, euler #=-2 (125524,376446,250920) : difference with theory (-2) = 0 CORRECTING DEFECT 21 (vertices=67, convex hull=73) After retessellation of defect 21, euler #=-1 (125560,376585,251024) : difference with theory (-1) = 0 CORRECTING DEFECT 22 (vertices=69, convex hull=96) After retessellation of defect 22, euler #=0 (125593,376727,251134) : difference with theory (0) = 0 CORRECTING DEFECT 23 (vertices=25, convex hull=59) After retessellation of defect 23, euler #=1 (125601,376776,251176) : difference with theory (1) = 0 CORRECTING DEFECT 24 (vertices=66, convex hull=55) After retessellation of defect 24, euler #=2 (125616,376842,251228) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->6.70) (max @ vno 105121 --> 105127) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->6.70) (max @ vno 105121 --> 105127) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 74 mutations (35.1%), 137 crossovers (64.9%), 84 vertices were eliminated building final representation... 1232 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125616, nf=251228, ne=376842, g=0) writing corrected surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.1 minutes 0 defective edges removing intersecting faces 000: 116 intersecting 001: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 125616 - 376842 + 251228 = 2 --> 0 holes F =2V-4: 251228 = 251232-4 (0) 2E=3F: 753684 = 753684 (0) total defect index = 0 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 17 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Mar 22 05:14:39 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs good_output_5.1 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... 10884 bright wm thresholded. 2360 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.orig... computing class statistics... border white: 235150 voxels (1.40%) border gray 264987 voxels (1.58%) WM (91.0): 92.7 +- 9.0 [70.0 --> 110.0] GM (77.0) : 75.3 +- 12.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.5 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 37.0 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->2.83) (max @ vno 105127 --> 105129) face area 0.28 +- 0.12 (0.00-->1.79) mean absolute distance = 0.86 +- 1.03 3408 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=62 using class modes intead of means.... mean inside = 91.5, mean outside = 71.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=73.5, 83 (83) missing vertices, mean dist 0.4 [0.8 (%24.9)->0.9 (%75.1))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.02-->3.79) (max @ vno 95366 --> 96225) face area 0.28 +- 0.14 (0.00-->2.02) mean absolute distance = 0.41 +- 0.75 2830 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5964878.0, rms=12.67 001: dt: 0.5000, sse=5888002.5, rms=9.45 002: dt: 0.5000, sse=5990449.0, rms=7.36 003: dt: 0.5000, sse=6220580.5, rms=5.89 004: dt: 0.5000, sse=6325783.0, rms=4.94 005: dt: 0.5000, sse=6534012.0, rms=4.33 006: dt: 0.5000, sse=6607812.0, rms=3.99 007: dt: 0.5000, sse=6742140.0, rms=3.79 008: dt: 0.5000, sse=6740792.5, rms=3.69 009: dt: 0.5000, sse=6799899.5, rms=3.60 rms = 3.58, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6744756.0, rms=3.58 011: dt: 0.2500, sse=4088283.2, rms=2.38 012: dt: 0.2500, sse=3695681.2, rms=2.04 013: dt: 0.2500, sse=3522488.0, rms=1.96 014: dt: 0.2500, sse=3464418.5, rms=1.90 rms = 1.88, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3429941.0, rms=1.88 016: dt: 0.1250, sse=3361022.2, rms=1.82 rms = 1.81, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3340365.8, rms=1.81 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.2, 35 (10) missing vertices, mean dist -0.3 [0.5 (%71.9)->0.3 (%28.1))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.12-->3.27) (max @ vno 50024 --> 51136) face area 0.36 +- 0.17 (0.00-->2.51) mean absolute distance = 0.31 +- 0.46 2863 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063636.0, rms=5.32 018: dt: 0.5000, sse=4334290.5, rms=3.28 rms = 3.40, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3986066.8, rms=2.55 020: dt: 0.2500, sse=3820483.8, rms=1.95 021: dt: 0.2500, sse=3690735.5, rms=1.67 022: dt: 0.2500, sse=3643902.0, rms=1.58 rms = 1.54, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3603528.2, rms=1.54 024: dt: 0.1250, sse=3553583.5, rms=1.49 rms = 1.49, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3532453.8, rms=1.49 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.7, 33 (7) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %78 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.10-->3.56) (max @ vno 50024 --> 51136) face area 0.35 +- 0.17 (0.00-->2.50) mean absolute distance = 0.24 +- 0.35 2893 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3932737.5, rms=4.46 026: dt: 0.5000, sse=4138729.2, rms=2.95 rms = 3.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3833551.0, rms=2.00 028: dt: 0.2500, sse=3730839.8, rms=1.55 029: dt: 0.2500, sse=3705124.0, rms=1.38 rms = 1.38, time step reduction 2 of 3 to 0.125... rms = 1.35, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3677782.0, rms=1.35 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.1, 34 (7) missing vertices, mean dist -0.1 [0.3 (%58.8)->0.2 (%41.2))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3729450.2, rms=2.13 rms = 2.28, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3763192.8, rms=1.45 032: dt: 0.2500, sse=3910226.0, rms=1.02 rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3907519.2, rms=1.01 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 1748 vertices erasing segment 1 (vno[0] = 77481) erasing segment 2 (vno[0] = 79343) erasing segment 3 (vno[0] = 81235) erasing segment 4 (vno[0] = 82346) erasing segment 5 (vno[0] = 84335) erasing segment 6 (vno[0] = 85190) erasing segment 7 (vno[0] = 88177) erasing segment 8 (vno[0] = 89102) erasing segment 9 (vno[0] = 90064) erasing segment 10 (vno[0] = 92790) erasing segment 11 (vno[0] = 95393) erasing segment 12 (vno[0] = 96274) erasing segment 13 (vno[0] = 97681) writing cortex label to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/rh.cortex.label... LabelWrite: saving to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/rh.cortex.label writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.area vertex spacing 0.90 +- 0.25 (0.06-->3.70) (max @ vno 50025 --> 51136) face area 0.34 +- 0.16 (0.00-->2.47) refinement took 5.7 minutes #-------------------------------------------- #@# Smooth2 rh Tue Mar 22 05:20:25 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Mar 22 05:20:31 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.9 mm, total surface area = 78588 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 288 vertices thresholded to be in k1 ~ [-0.27 0.37], k2 ~ [-0.09 0.07] total integrated curvature = 0.571*4pi (7.174) --> 0 handles ICI = 1.5, FI = 9.8, variation=166.514 148 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 130 vertices thresholded to be in [-0.13 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Tue Mar 22 05:22:40 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm good_output_5.1 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ good_output_5.1/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 234 ] Gb_filter = 0 WARN: S lookup min: -0.072377 WARN: S explicit min: 0.000000 vertex = 25 #-------------------------------------------- #@# Sphere rh Tue Mar 22 05:22:48 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 0.83 hours scaling brain by 0.292... pass 1: epoch 1 of 3 starting distance error %18.92 pass 1: epoch 2 of 3 starting distance error %18.90 unfolding complete - removing small folds... starting distance error %18.84 removing remaining folds... final distance error %18.86 #-------------------------------------------- #@# Surf Reg rh Tue Mar 22 06:12:55 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable5/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/stable5/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.587 curvature mean = 0.042, std = 0.937 curvature mean = 0.018, std = 0.871 curvature mean = 0.026, std = 0.957 curvature mean = 0.008, std = 0.947 curvature mean = 0.021, std = 0.968 curvature mean = 0.004, std = 0.977 curvature mean = 0.020, std = 0.969 curvature mean = 0.001, std = 0.990 curvature mean = -0.024, std = 0.271 curvature mean = 0.006, std = 0.071 curvature mean = 0.060, std = 0.374 curvature mean = 0.006, std = 0.084 curvature mean = 0.027, std = 0.572 curvature mean = 0.006, std = 0.090 curvature mean = 0.015, std = 0.708 curvature mean = 0.006, std = 0.093 curvature mean = 0.005, std = 0.807 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Mar 22 06:50:11 EDT 2011 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Mar 22 06:50:14 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Mar 22 06:50:18 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output_5.1 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading atlas from /usr/local/freesurfer/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1041 labels changed using aseg relabeling using gibbs priors... 000: 2851 changed, 125616 examined... 001: 657 changed, 12071 examined... 002: 138 changed, 3645 examined... 003: 52 changed, 826 examined... 004: 20 changed, 328 examined... 005: 2 changed, 109 examined... 006: 1 changed, 14 examined... 007: 0 changed, 7 examined... 151 labels changed using aseg 000: 90 total segments, 50 labels (316 vertices) changed 001: 46 total segments, 7 labels (18 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1498 vertices marked for relabeling... 1498 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 55 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Mar 22 06:51:14 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs good_output_5.1 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... 10884 bright wm thresholded. 2360 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.orig... computing class statistics... border white: 235150 voxels (1.40%) border gray 264987 voxels (1.58%) WM (91.0): 92.7 +- 9.0 [70.0 --> 110.0] GM (77.0) : 75.3 +- 12.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.5 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 37.0 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.6 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=62 using class modes intead of means.... mean inside = 91.5, mean outside = 71.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->2.83) (max @ vno 105127 --> 105129) face area 0.28 +- 0.12 (0.00-->1.79) mean absolute distance = 0.86 +- 1.04 3490 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 386 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown mean border=73.5, 87 (87) missing vertices, mean dist 0.4 [0.9 (%24.9)->0.9 (%75.1))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.02-->3.79) (max @ vno 95366 --> 96225) face area 0.28 +- 0.14 (0.00-->2.02) mean absolute distance = 0.41 +- 0.75 2865 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5976879.5, rms=12.66 001: dt: 0.5000, sse=5899865.5, rms=9.44 002: dt: 0.5000, sse=6003367.5, rms=7.35 003: dt: 0.5000, sse=6236423.5, rms=5.89 004: dt: 0.5000, sse=6345334.5, rms=4.93 005: dt: 0.5000, sse=6552051.0, rms=4.32 006: dt: 0.5000, sse=6628694.0, rms=3.99 007: dt: 0.5000, sse=6760493.0, rms=3.78 008: dt: 0.5000, sse=6764606.5, rms=3.69 009: dt: 0.5000, sse=6819612.0, rms=3.60 rms = 3.57, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6765406.5, rms=3.57 011: dt: 0.2500, sse=4098836.2, rms=2.38 012: dt: 0.2500, sse=3706629.0, rms=2.04 013: dt: 0.2500, sse=3533799.0, rms=1.96 014: dt: 0.2500, sse=3475079.8, rms=1.90 rms = 1.88, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3441231.8, rms=1.88 016: dt: 0.1250, sse=3372931.5, rms=1.82 rms = 1.81, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3351758.5, rms=1.81 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 4 with 306 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown mean border=77.2, 35 (10) missing vertices, mean dist -0.3 [0.5 (%71.8)->0.3 (%28.2))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.12-->3.27) (max @ vno 50024 --> 51136) face area 0.36 +- 0.17 (0.00-->2.51) mean absolute distance = 0.31 +- 0.46 2875 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4077561.8, rms=5.32 018: dt: 0.5000, sse=4348131.5, rms=3.28 rms = 3.40, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3998497.8, rms=2.55 020: dt: 0.2500, sse=3831675.0, rms=1.95 021: dt: 0.2500, sse=3701154.5, rms=1.67 022: dt: 0.2500, sse=3653206.0, rms=1.58 rms = 1.54, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3612043.8, rms=1.54 024: dt: 0.1250, sse=3562348.0, rms=1.49 rms = 1.49, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3540977.0, rms=1.49 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 260 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown mean border=80.7, 32 (7) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.08-->3.56) (max @ vno 50024 --> 51136) face area 0.35 +- 0.16 (0.00-->2.50) mean absolute distance = 0.24 +- 0.35 2910 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3942916.5, rms=4.46 026: dt: 0.5000, sse=4146179.5, rms=2.94 rms = 3.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3840701.2, rms=2.00 028: dt: 0.2500, sse=3737166.0, rms=1.55 029: dt: 0.2500, sse=3711657.2, rms=1.38 rms = 1.38, time step reduction 2 of 3 to 0.125... rms = 1.35, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3684272.8, rms=1.35 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 298 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown mean border=82.0, 35 (7) missing vertices, mean dist -0.1 [0.3 (%58.8)->0.2 (%41.2))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3736494.5, rms=2.12 rms = 2.27, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3770732.2, rms=1.45 032: dt: 0.2500, sse=3918224.8, rms=1.02 rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3915689.8, rms=1.01 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=52.1, 31 (31) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.1 (%100.0))] %22 local maxima, %61 large gradients and %11 min vals, 935 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=23195372.0, rms=29.52 001: dt: 0.5000, sse=17187680.0, rms=24.89 002: dt: 0.5000, sse=12814177.0, rms=20.91 003: dt: 0.5000, sse=9825831.0, rms=17.62 004: dt: 0.5000, sse=8165615.5, rms=14.91 005: dt: 0.5000, sse=7180283.0, rms=12.64 006: dt: 0.5000, sse=6566315.5, rms=10.78 007: dt: 0.5000, sse=6127810.5, rms=9.17 008: dt: 0.5000, sse=5881954.5, rms=7.75 009: dt: 0.5000, sse=5718693.0, rms=6.56 010: dt: 0.5000, sse=5723156.0, rms=5.61 011: dt: 0.5000, sse=5784063.0, rms=4.92 012: dt: 0.5000, sse=5887867.5, rms=4.45 013: dt: 0.5000, sse=5958763.5, rms=4.17 014: dt: 0.5000, sse=6050893.0, rms=3.99 015: dt: 0.5000, sse=6093421.0, rms=3.89 016: dt: 0.5000, sse=6104994.5, rms=3.81 rms = 3.77, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6141526.0, rms=3.77 018: dt: 0.2500, sse=4038946.0, rms=2.88 019: dt: 0.2500, sse=3781193.2, rms=2.65 rms = 2.61, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3659244.5, rms=2.61 021: dt: 0.1250, sse=3534683.8, rms=2.51 rms = 2.51, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3511542.8, rms=2.51 positioning took 2.3 minutes mean border=49.0, 340 (5) missing vertices, mean dist 0.2 [0.2 (%44.2)->0.6 (%55.8))] %48 local maxima, %40 large gradients and % 7 min vals, 243 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4314068.5, rms=5.63 023: dt: 0.5000, sse=4416420.0, rms=4.13 024: dt: 0.5000, sse=5518469.5, rms=3.90 rms = 3.95, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=4534399.5, rms=3.13 026: dt: 0.2500, sse=4181566.8, rms=2.79 027: dt: 0.2500, sse=4100137.8, rms=2.68 rms = 2.64, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4069922.8, rms=2.64 029: dt: 0.1250, sse=3964725.2, rms=2.54 rms = 2.52, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3953640.5, rms=2.52 positioning took 0.8 minutes mean border=46.3, 436 (2) missing vertices, mean dist 0.2 [0.2 (%37.8)->0.4 (%62.2))] %65 local maxima, %23 large gradients and % 7 min vals, 298 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4259841.5, rms=4.24 031: dt: 0.5000, sse=4383281.0, rms=3.72 rms = 3.75, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4111080.0, rms=2.91 033: dt: 0.2500, sse=4199619.0, rms=2.55 034: dt: 0.2500, sse=4176976.5, rms=2.46 rms = 2.42, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4186860.5, rms=2.42 036: dt: 0.1250, sse=4082769.2, rms=2.31 rms = 2.30, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4073368.2, rms=2.30 positioning took 0.7 minutes mean border=44.9, 986 (2) missing vertices, mean dist 0.1 [0.2 (%44.2)->0.3 (%55.8))] %72 local maxima, %16 large gradients and % 6 min vals, 280 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4146015.5, rms=2.88 rms = 3.35, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4028845.2, rms=2.46 039: dt: 0.2500, sse=4089712.5, rms=2.28 040: dt: 0.2500, sse=4155984.0, rms=2.21 rms = 2.17, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4213104.0, rms=2.17 042: dt: 0.1250, sse=4123444.5, rms=2.10 rms = 2.08, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4122583.0, rms=2.08 positioning took 0.7 minutes writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.area.pial vertex spacing 1.02 +- 0.41 (0.05-->6.31) (max @ vno 93599 --> 92725) face area 0.41 +- 0.29 (0.00-->5.05) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 125616 vertices processed 25000 of 125616 vertices processed 50000 of 125616 vertices processed 75000 of 125616 vertices processed 100000 of 125616 vertices processed 125000 of 125616 vertices processed 0 of 125616 vertices processed 25000 of 125616 vertices processed 50000 of 125616 vertices processed 75000 of 125616 vertices processed 100000 of 125616 vertices processed 125000 of 125616 vertices processed thickness calculation complete, 356:573 truncations. 60593 vertices at 0 distance 81140 vertices at 1 distance 63215 vertices at 2 distance 22169 vertices at 3 distance 6745 vertices at 4 distance 2310 vertices at 5 distance 934 vertices at 6 distance 455 vertices at 7 distance 225 vertices at 8 distance 147 vertices at 9 distance 71 vertices at 10 distance 56 vertices at 11 distance 26 vertices at 12 distance 24 vertices at 13 distance 22 vertices at 14 distance 19 vertices at 15 distance 13 vertices at 16 distance 7 vertices at 17 distance 2 vertices at 18 distance 4 vertices at 19 distance 3 vertices at 20 distance writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.thickness positioning took 11.2 minutes #-------------------------------------------- #@# Surf Volume rh Tue Mar 22 07:02:25 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Tue Mar 22 07:02:28 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab good_output_5.1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1336 922 2498 2.664 0.506 0.123 0.037 13 1.9 bankssts 970 664 1863 2.582 0.560 0.163 0.053 28 2.2 caudalanteriorcingulate 3064 2153 5823 2.441 0.495 0.137 0.047 39 6.2 caudalmiddlefrontal 1936 1266 2540 1.786 0.459 0.172 0.067 37 5.4 cuneus 540 387 1779 3.231 0.739 0.143 0.042 6 0.8 entorhinal 4599 3247 8726 2.337 0.680 0.144 0.047 76 8.5 fusiform 8223 5738 15602 2.420 0.604 0.150 0.055 165 18.3 inferiorparietal 4107 2843 8809 2.546 0.730 0.144 0.052 65 8.6 inferiortemporal 1263 818 2111 2.414 0.844 0.145 0.050 19 2.6 isthmuscingulate 6402 4365 10288 2.098 0.525 0.161 0.064 116 15.4 lateraloccipital 3821 2615 6653 2.279 0.703 0.144 0.065 64 10.5 lateralorbitofrontal 3644 2614 4958 1.752 0.494 0.153 0.051 52 7.3 lingual 2945 2057 5064 2.156 0.648 0.151 0.062 63 7.3 medialorbitofrontal 5066 3516 11352 2.669 0.650 0.147 0.071 114 12.5 middletemporal 1068 707 2324 2.596 1.068 0.101 0.030 7 1.3 parahippocampal 2348 1540 3551 2.122 0.535 0.119 0.167 30 3.8 paracentral 2277 1544 4247 2.471 0.476 0.135 0.040 29 3.5 parsopercularis 1056 701 2201 2.525 0.491 0.162 0.066 19 2.8 parsorbitalis 1851 1288 3620 2.436 0.513 0.144 0.057 28 3.8 parstriangularis 1630 1111 1714 1.583 0.358 0.136 0.045 16 2.9 pericalcarine 5019 3411 7397 1.906 0.636 0.128 0.042 56 9.0 postcentral 1666 1174 3195 2.428 0.569 0.161 0.060 34 3.9 posteriorcingulate 6891 4482 12145 2.452 0.564 0.120 0.038 64 11.0 precentral 5682 3865 9459 2.259 0.642 0.153 0.077 124 16.5 precuneus 727 477 1472 2.692 0.632 0.129 0.044 10 1.1 rostralanteriorcingulate 6939 4923 13235 2.290 0.582 0.152 0.057 124 15.9 rostralmiddlefrontal 8771 6095 17475 2.478 0.569 0.147 0.058 146 20.7 superiorfrontal 7544 5028 11320 2.046 0.509 0.132 0.043 92 12.8 superiorparietal 5163 3573 10166 2.521 0.645 0.131 0.044 71 9.2 superiortemporal 5691 3790 10092 2.371 0.577 0.135 0.054 80 11.9 supramarginal 287 193 790 2.736 0.556 0.205 0.108 9 1.1 frontalpole 474 361 1876 3.540 0.465 0.157 0.059 6 1.1 temporalpole 496 310 722 2.080 0.333 0.135 0.047 6 0.9 transversetemporal 3572 2374 6989 2.756 0.884 0.135 0.089 137 10.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Mar 22 07:02:47 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output_5.1 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693 2011/03/16 17:31:45 fischl Exp $ reading atlas from /usr/local/freesurfer/stable5/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 33 labels changed using aseg relabeling using gibbs priors... 000: 9238 changed, 125616 examined... 001: 2167 changed, 35158 examined... 002: 676 changed, 11177 examined... 003: 309 changed, 3795 examined... 004: 127 changed, 1726 examined... 005: 71 changed, 716 examined... 006: 38 changed, 383 examined... 007: 12 changed, 215 examined... 008: 7 changed, 77 examined... 009: 9 changed, 35 examined... 010: 3 changed, 34 examined... 011: 1 changed, 18 examined... 012: 2 changed, 7 examined... 013: 2 changed, 10 examined... 014: 1 changed, 12 examined... 015: 1 changed, 5 examined... 016: 3 changed, 7 examined... 017: 1 changed, 13 examined... 018: 1 changed, 7 examined... 019: 0 changed, 5 examined... 26 labels changed using aseg 000: 258 total segments, 174 labels (1835 vertices) changed 001: 92 total segments, 8 labels (28 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 150 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 923 vertices marked for relabeling... 923 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 1 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Mar 22 07:03:49 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab good_output_5.1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 645 478 1294 2.298 0.562 0.172 0.070 14 1.6 G_and_S_frontomargin 1284 912 2663 2.436 0.602 0.165 0.059 23 3.2 G_and_S_occipital_inf 1344 883 2176 2.028 0.522 0.131 0.043 15 2.4 G_and_S_paracentral 1163 790 2435 2.556 0.588 0.145 0.048 16 2.1 G_and_S_subcentral 901 620 1739 2.196 0.610 0.161 0.063 21 2.3 G_and_S_transv_frontopol 2602 1793 4792 2.435 0.592 0.134 0.045 38 4.7 G_and_S_cingul-Ant 1360 950 2566 2.377 0.548 0.144 0.049 25 3.0 G_and_S_cingul-Mid-Ant 1236 854 2135 2.277 0.533 0.131 0.041 15 2.0 G_and_S_cingul-Mid-Post 604 392 1456 2.875 0.518 0.190 0.077 16 1.8 G_cingul-Post-dorsal 258 176 492 2.386 0.810 0.158 0.076 4 0.7 G_cingul-Post-ventral 1843 1196 2429 1.769 0.435 0.174 0.069 37 5.3 G_cuneus 1191 809 2755 2.629 0.461 0.155 0.053 22 2.5 G_front_inf-Opercular 253 176 630 2.713 0.360 0.182 0.079 7 0.8 G_front_inf-Orbital 926 652 2264 2.631 0.480 0.154 0.073 18 2.2 G_front_inf-Triangul 3807 2756 8676 2.474 0.551 0.165 0.066 81 10.6 G_front_middle 6064 4159 13507 2.601 0.567 0.164 0.123 139 17.8 G_front_sup 469 321 1130 2.971 0.766 0.129 0.044 7 0.8 G_Ins_lg_and_S_cent_ins 573 384 1751 3.337 0.750 0.197 0.139 25 2.1 G_insular_short 1893 1310 4020 2.443 0.560 0.169 0.064 38 4.9 G_occipital_middle 1686 1123 2749 2.095 0.597 0.153 0.059 28 3.8 G_occipital_sup 1866 1299 4098 2.552 0.567 0.151 0.060 41 4.4 G_oc-temp_lat-fusifor 2143 1541 3189 1.789 0.524 0.159 0.057 33 4.8 G_oc-temp_med-Lingual 1813 1230 4766 3.052 0.979 0.149 0.116 105 6.7 G_oc-temp_med-Parahip 2646 1798 5804 2.484 0.742 0.165 0.083 62 9.4 G_orbital 3083 2160 7516 2.729 0.575 0.183 0.080 111 9.8 G_pariet_inf-Angular 2966 1972 6002 2.524 0.561 0.148 0.072 55 8.1 G_pariet_inf-Supramar 2203 1475 4004 2.196 0.468 0.142 0.047 35 4.0 G_parietal_sup 1867 1251 3072 1.993 0.567 0.137 0.055 25 4.6 G_postcentral 2611 1682 5894 2.711 0.450 0.137 0.048 33 5.3 G_precentral 2870 1940 5698 2.415 0.642 0.170 0.107 95 11.8 G_precuneus 820 606 1793 2.341 0.460 0.212 0.117 31 3.9 G_rectus 264 171 460 2.607 0.594 0.095 0.031 2 0.3 G_subcallosal 383 237 631 2.157 0.326 0.139 0.054 6 0.8 G_temp_sup-G_T_transv 1842 1288 4868 2.854 0.576 0.158 0.064 38 4.9 G_temp_sup-Lateral 733 516 1509 2.647 0.763 0.097 0.025 4 0.7 G_temp_sup-Plan_polar 727 488 1305 2.344 0.520 0.116 0.035 6 1.0 G_temp_sup-Plan_tempo 2195 1562 5813 2.752 0.732 0.171 0.067 48 6.1 G_temporal_inf 3142 2227 8180 2.809 0.642 0.167 0.101 99 10.3 G_temporal_middle 368 249 533 2.259 0.432 0.117 0.026 2 0.4 Lat_Fis-ant-Horizont 167 114 291 2.429 0.654 0.141 0.042 2 0.3 Lat_Fis-ant-Vertical 1450 970 1966 2.323 0.552 0.111 0.027 9 1.6 Lat_Fis-post 3025 2043 4526 1.888 0.479 0.168 0.074 61 8.0 Pole_occipital 1588 1124 4734 3.053 0.652 0.161 0.059 31 3.7 Pole_temporal 1560 1064 1840 1.944 0.754 0.132 0.038 15 2.4 S_calcarine 2958 1957 3361 1.883 0.681 0.107 0.028 18 3.5 S_central 1396 974 1958 2.070 0.516 0.111 0.029 10 1.7 S_cingul-Marginalis 733 484 1100 2.526 0.730 0.113 0.032 5 1.0 S_circular_insula_ant 1224 779 1631 2.247 0.714 0.082 0.024 8 1.1 S_circular_insula_inf 1332 899 1906 2.294 0.451 0.115 0.029 8 1.6 S_circular_insula_sup 968 669 1350 2.018 0.631 0.107 0.022 6 0.9 S_collat_transv_ant 670 451 714 1.776 0.342 0.141 0.045 7 1.2 S_collat_transv_post 2267 1525 3451 2.257 0.449 0.128 0.043 26 3.6 S_front_inf 1268 901 2333 2.259 0.628 0.137 0.055 18 2.9 S_front_middle 2207 1555 3304 2.179 0.483 0.115 0.029 16 2.8 S_front_sup 850 558 1111 2.083 0.417 0.115 0.032 6 1.1 S_interm_prim-Jensen 3177 2141 3892 1.955 0.431 0.117 0.032 25 4.3 S_intrapariet_and_P_trans 1156 767 1603 2.065 0.482 0.134 0.042 13 1.9 S_oc_middle_and_Lunatus 1619 1095 1956 1.911 0.447 0.119 0.033 12 2.1 S_oc_sup_and_transversal 651 441 954 2.221 0.517 0.135 0.041 7 1.2 S_occipital_ant 835 582 1074 2.064 0.517 0.136 0.040 9 1.3 S_oc-temp_lat 2008 1451 2579 1.802 0.588 0.117 0.029 18 2.2 S_oc-temp_med_and_Lingual 506 349 701 1.958 0.465 0.124 0.038 4 0.7 S_orbital_lateral 998 692 1260 1.815 0.685 0.100 0.023 6 0.9 S_orbital_med-olfact 1300 895 2106 2.325 0.611 0.140 0.056 16 2.8 S_orbital-H_Shaped 2121 1426 2508 1.932 0.563 0.147 0.053 26 4.3 S_parieto_occipital 1316 819 1442 2.264 0.754 0.152 0.052 31 2.7 S_pericallosal 1694 1140 2021 1.844 0.534 0.112 0.029 12 2.0 S_postcentral 1631 1106 2422 2.324 0.400 0.112 0.028 11 2.0 S_precentral-inf-part 955 663 1344 2.301 0.433 0.116 0.030 6 1.2 S_precentral-sup-part 403 275 514 1.895 0.754 0.102 0.022 3 0.4 S_suborbital 940 667 1628 2.251 0.479 0.135 0.047 11 1.6 S_subparietal 1097 725 1524 2.525 0.494 0.124 0.033 8 1.6 S_temporal_inf 6040 4190 9726 2.363 0.553 0.120 0.034 57 7.9 S_temporal_sup 314 236 429 2.054 0.472 0.155 0.040 3 0.6 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Tue Mar 22 07:04:10 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon good_output_5.1 SUBJECTS_DIR is /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 18 writing volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Mar 22 07:19:58 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject good_output_5.1 $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject good_output_5.1 sysname Linux hostname compute-0-1.local machine x86_64 user khoa atlas_icv (eTIV) = 1513067 mm^3 (det: 1.287521 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 219586 rh white matter volume 225253 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 250984.518045, pTot = 456076.015694 c = 205091.497649 rh surface-based volumes (mm3): wTot = 258666.624451, pTot = 465116.442090 c = 206449.817639 Computing SupraTentVolCor SupraTentVolCor = 61652.000 SupraTentVol = 982844.458 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 17048 17048 4 5 Left-Inf-Lat-Vent 970 970 5 7 Left-Cerebellum-White-Matter 11012 11012 6 8 Left-Cerebellum-Cortex 42072 42072 7 10 Left-Thalamus-Proper 6046 6046 8 11 Left-Caudate 5091 5091 9 12 Left-Putamen 5237 5237 10 13 Left-Pallidum 1530 1530 11 14 3rd-Ventricle 1557 1557 12 15 4th-Ventricle 2007 2007 13 16 Brain-Stem 17388 17388 14 17 Left-Hippocampus 4025 4025 15 18 Left-Amygdala 1408 1408 16 24 CSF 1060 1060 17 26 Left-Accumbens-area 562 562 18 28 Left-VentralDC 3093 3093 19 30 Left-vessel 93 93 20 31 Left-choroid-plexus 1985 1985 23 43 Right-Lateral-Ventricle 20012 20012 24 44 Right-Inf-Lat-Vent 957 957 25 46 Right-Cerebellum-White-Matter 11311 11311 26 47 Right-Cerebellum-Cortex 42943 42943 27 49 Right-Thalamus-Proper 6055 6055 28 50 Right-Caudate 4809 4809 29 51 Right-Putamen 5124 5124 30 52 Right-Pallidum 1462 1462 31 53 Right-Hippocampus 4160 4160 32 54 Right-Amygdala 1628 1628 33 58 Right-Accumbens-area 694 694 34 60 Right-VentralDC 3326 3326 35 62 Right-vessel 130 130 36 63 Right-choroid-plexus 2240 2240 37 72 5th-Ventricle 48 48 38 77 WM-hypointensities 4558 4558 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 137 137 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 331 331 45 251 CC_Posterior 955 955 46 252 CC_Mid_Posterior 273 273 47 253 CC_Central 339 339 48 254 CC_Mid_Anterior 337 337 49 255 CC_Anterior 710 710 Reporting on 45 segmentations SubCortGrayVol = 156653 #----------------------------------------- #@# AParc-to-ASeg Tue Mar 22 07:30:52 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_aparc2aseg --s good_output_5.1 --volmask SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output_5.1 outvol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 404669 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aparc+aseg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_aparc2aseg --s good_output_5.1 --volmask --a2009s SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output_5.1 outvol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 404669 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Mar 22 07:34:08 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_aparc2aseg --s good_output_5.1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output_5.1 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aparc+aseg.mgz Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/ribbon.mgz Loading filled from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8564 vertices from left hemi Ripped 8548 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aseg.mgz Loading Ctx Seg File /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 825547 Used brute-force search on 148 voxels Fixing Parahip LH WM Found 19 clusters 0 k 2.000000 1 k 1.000000 2 k 2.000000 3 k 1458.000000 4 k 3.000000 5 k 1.000000 6 k 3.000000 7 k 1.000000 8 k 1.000000 9 k 6.000000 10 k 2.000000 11 k 6.000000 12 k 1.000000 13 k 1.000000 14 k 1.000000 15 k 1.000000 16 k 1.000000 17 k 1.000000 18 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 30.000000 5 k 1561.000000 6 k 1.000000 7 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject good_output_5.1 --surf-wm-vol --ctab /usr/local/freesurfer/stable5/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject good_output_5.1 --surf-wm-vol --ctab /usr/local/freesurfer/stable5/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-1.local machine x86_64 user khoa atlas_icv (eTIV) = 1513067 mm^3 (det: 1.287521 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 219586 rh white matter volume 225253 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1513344 # brainmaskvolume 1513344.0 # nbrainsegvoxels 226967 # brainsegvolume 226967.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 3679 3679 2 3002 wm-lh-caudalanteriorcingulate 2956 2956 3 3003 wm-lh-caudalmiddlefrontal 6333 6333 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 1741 1741 6 3006 wm-lh-entorhinal 803 803 7 3007 wm-lh-fusiform 6631 6631 8 3008 wm-lh-inferiorparietal 9266 9266 9 3009 wm-lh-inferiortemporal 6119 6119 10 3010 wm-lh-isthmuscingulate 3484 3484 11 3011 wm-lh-lateraloccipital 6911 6911 12 3012 wm-lh-lateralorbitofrontal 5504 5504 13 3013 wm-lh-lingual 4658 4658 14 3014 wm-lh-medialorbitofrontal 4098 4098 15 3015 wm-lh-middletemporal 5657 5657 16 3016 wm-lh-parahippocampal 1583 1583 17 3017 wm-lh-paracentral 3627 3627 18 3018 wm-lh-parsopercularis 3005 3005 19 3019 wm-lh-parsorbitalis 935 935 20 3020 wm-lh-parstriangularis 2412 2412 21 3021 wm-lh-pericalcarine 1874 1874 22 3022 wm-lh-postcentral 7444 7444 23 3023 wm-lh-posteriorcingulate 4119 4119 24 3024 wm-lh-precentral 11912 11912 25 3025 wm-lh-precuneus 8611 8611 26 3026 wm-lh-rostralanteriorcingulate 2342 2342 27 3027 wm-lh-rostralmiddlefrontal 10569 10569 28 3028 wm-lh-superiorfrontal 15441 15441 29 3029 wm-lh-superiorparietal 12177 12177 30 3030 wm-lh-superiortemporal 7635 7635 31 3031 wm-lh-supramarginal 9014 9014 32 3032 wm-lh-frontalpole 232 232 33 3033 wm-lh-temporalpole 681 681 34 3034 wm-lh-transversetemporal 760 760 35 3035 wm-lh-insula 9995 9995 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2859 2859 120 4002 wm-rh-caudalanteriorcingulate 2509 2509 121 4003 wm-rh-caudalmiddlefrontal 6331 6331 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1881 1881 124 4006 wm-rh-entorhinal 778 778 125 4007 wm-rh-fusiform 6649 6649 126 4008 wm-rh-inferiorparietal 12724 12724 127 4009 wm-rh-inferiortemporal 5014 5014 128 4010 wm-rh-isthmuscingulate 3428 3428 129 4011 wm-rh-lateraloccipital 8235 8235 130 4012 wm-rh-lateralorbitofrontal 6293 6293 131 4013 wm-rh-lingual 4290 4290 132 4014 wm-rh-medialorbitofrontal 3452 3452 133 4015 wm-rh-middletemporal 6430 6430 134 4016 wm-rh-parahippocampal 1721 1721 135 4017 wm-rh-paracentral 4757 4757 136 4018 wm-rh-parsopercularis 3737 3737 137 4019 wm-rh-parsorbitalis 1010 1010 138 4020 wm-rh-parstriangularis 2749 2749 139 4021 wm-rh-pericalcarine 2114 2114 140 4022 wm-rh-postcentral 6139 6139 141 4023 wm-rh-posteriorcingulate 3854 3854 142 4024 wm-rh-precentral 12772 12772 143 4025 wm-rh-precuneus 9420 9420 144 4026 wm-rh-rostralanteriorcingulate 1913 1913 145 4027 wm-rh-rostralmiddlefrontal 10706 10706 146 4028 wm-rh-superiorfrontal 15760 15760 147 4029 wm-rh-superiorparietal 11738 11738 148 4030 wm-rh-superiortemporal 6693 6693 149 4031 wm-rh-supramarginal 9312 9312 150 4032 wm-rh-frontalpole 211 211 151 4033 wm-rh-temporalpole 536 536 152 4034 wm-rh-transversetemporal 517 517 153 4035 wm-rh-insula 9118 9118 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 25871 25871 237 5002 Right-UnsegmentedWhiteMatter 26470 26470 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label #-------------------------------------------- #@# BA Labels lh Tue Mar 22 07:52:51 EDT 2011 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA1.label --trgsubject good_output_5.1 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 339 Checking for and removing duplicates Writing label file ./lh.BA1.label LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA2.label --trgsubject good_output_5.1 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 880 Checking for and removing duplicates Writing label file ./lh.BA2.label LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3a.label --trgsubject good_output_5.1 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./lh.BA3a.label LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3b.label --trgsubject good_output_5.1 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 386 Checking for and removing duplicates Writing label file ./lh.BA3b.label LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4a.label --trgsubject good_output_5.1 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./lh.BA4a.label LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4p.label --trgsubject good_output_5.1 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA4p.label LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA6.label --trgsubject good_output_5.1 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 716 Checking for and removing duplicates Writing label file ./lh.BA6.label LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA44.label --trgsubject good_output_5.1 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 346 Checking for and removing duplicates Writing label file ./lh.BA44.label LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA45.label --trgsubject good_output_5.1 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 493 Checking for and removing duplicates Writing label file ./lh.BA45.label LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V1.label --trgsubject good_output_5.1 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 534 Checking for and removing duplicates Writing label file ./lh.V1.label LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V2.label --trgsubject good_output_5.1 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 1881 Checking for and removing duplicates Writing label file ./lh.V2.label LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.MT.label --trgsubject good_output_5.1 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./lh.MT.label LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s good_output_5.1 --hemi lh --ctab /usr/local/freesurfer/stable5/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' Reading ctab /usr/local/freesurfer/stable5/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label cmdline mris_label2annot --s good_output_5.1 --hemi lh --ctab /usr/local/freesurfer/stable5/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user khoa subject good_output_5.1 hemi lh SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs ColorTable /usr/local/freesurfer/stable5/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.orig input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 1 1530880 BA1 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 2 16749699 BA2 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 3 16711680 BA3a input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 4 3368703 BA3b input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 5 1376196 BA4a input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 6 13382655 BA4p input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 7 10036737 BA6 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 8 2490521 BA44 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 9 39283 BA45 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 10 3993 V1 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 88973 unhit vertices Writing annot to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab good_output_5.1 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /usr/local/freesurfer/stable5/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1057 639 1647 2.063 0.483 0.167 0.076 41 3.5 BA1 4337 2878 6661 2.149 0.512 0.137 0.048 63 8.9 BA2 965 650 899 1.738 0.376 0.122 0.031 7 1.3 BA3a 2498 1729 3643 1.824 0.583 0.124 0.038 28 3.7 BA3b 1577 967 2833 2.520 0.456 0.121 0.055 18 3.5 BA4a 1310 821 1990 2.503 0.466 0.103 0.046 11 2.0 BA4p 7546 5208 16136 2.656 0.561 0.143 0.061 128 18.9 BA6 2390 1638 4345 2.389 0.450 0.134 0.044 31 4.5 BA44 2673 1871 5280 2.356 0.501 0.157 0.056 49 5.9 BA45 2373 1628 2730 1.581 0.410 0.149 0.067 41 5.8 V1 6962 4749 9820 1.864 0.573 0.157 0.060 127 15.4 V2 1637 1114 2576 2.167 0.467 0.139 0.047 22 3.1 MT #-------------------------------------------- #@# BA Labels rh Tue Mar 22 07:55:17 EDT 2011 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA1.label --trgsubject good_output_5.1 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./rh.BA1.label LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA2.label --trgsubject good_output_5.1 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.BA2.label LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3a.label --trgsubject good_output_5.1 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 146 Checking for and removing duplicates Writing label file ./rh.BA3a.label LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3b.label --trgsubject good_output_5.1 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 178 Checking for and removing duplicates Writing label file ./rh.BA3b.label LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4a.label --trgsubject good_output_5.1 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./rh.BA4a.label LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4p.label --trgsubject good_output_5.1 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 229 Checking for and removing duplicates Writing label file ./rh.BA4p.label LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA6.label --trgsubject good_output_5.1 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 592 Checking for and removing duplicates Writing label file ./rh.BA6.label LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA44.label --trgsubject good_output_5.1 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 865 Checking for and removing duplicates Writing label file ./rh.BA44.label LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA45.label --trgsubject good_output_5.1 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 915 Checking for and removing duplicates Writing label file ./rh.BA45.label LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V1.label --trgsubject good_output_5.1 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 745 Checking for and removing duplicates Writing label file ./rh.V1.label LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V2.label --trgsubject good_output_5.1 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 2182 Checking for and removing duplicates Writing label file ./rh.V2.label LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.MT.label --trgsubject good_output_5.1 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = good_output_5.1 trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/stable5 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.MT.label LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s good_output_5.1 --hemi rh --ctab /usr/local/freesurfer/stable5/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' Reading ctab /usr/local/freesurfer/stable5/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label cmdline mris_label2annot --s good_output_5.1 --hemi rh --ctab /usr/local/freesurfer/stable5/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user khoa subject good_output_5.1 hemi rh SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs ColorTable /usr/local/freesurfer/stable5/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.orig input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 1 1530880 BA1 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 2 16749699 BA2 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 3 16711680 BA3a input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 4 3368703 BA3b input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 5 1376196 BA4a input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 6 13382655 BA4p input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 7 10036737 BA6 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 8 2490521 BA44 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 9 39283 BA45 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 10 3993 V1 input_transform: error reading transform. mris_label2annot: could not load transform file '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm' 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 90154 unhit vertices Writing annot to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab good_output_5.1 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /usr/local/freesurfer/stable5/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 705 419 1362 2.314 0.480 0.160 0.084 14 2.9 BA1 2420 1695 3525 1.953 0.573 0.119 0.034 21 3.4 BA2 1020 684 888 1.544 0.407 0.117 0.029 7 1.3 BA3a 1908 1314 2482 1.638 0.522 0.126 0.038 20 2.7 BA3b 1457 922 2615 2.415 0.567 0.115 0.247 19 2.4 BA4a 1357 838 2119 2.502 0.599 0.105 0.031 10 1.8 BA4p 6780 4561 13902 2.578 0.522 0.143 0.054 104 15.8 BA6 3836 2600 6669 2.412 0.473 0.127 0.037 41 5.8 BA44 4069 2768 7955 2.398 0.504 0.150 0.063 69 9.3 BA45 2818 1958 3520 1.647 0.416 0.156 0.054 41 6.2 V1 7541 5104 10540 1.899 0.509 0.158 0.062 129 17.7 V2 1551 1099 2800 2.273 0.572 0.154 0.052 24 3.0 MT /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Tue Mar 22 07:57:45 EDT 2011 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs; ln -s /usr/local/freesurfer/stable5/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o good_output_5.1 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject good_output_5.1. processing subject lh.EC_average... reading output surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 861 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label good_output_5.1 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/lh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 291 197 1130 3.430 0.449 0.128 0.035 3 0.5 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Tue Mar 22 07:58:08 EDT 2011 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... cd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs; ln -s /usr/local/freesurfer/stable5/subjects/rh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o good_output_5.1 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject good_output_5.1. processing subject rh.EC_average... reading output surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 841 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label good_output_5.1 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 330 208 1130 3.337 0.653 0.142 0.067 6 1.1 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s good_output_5.1 finished without error at Tue Mar 22 07:58:31 EDT 2011 New invocation of recon-all Mon Apr 25 12:04:15 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output /usr/local/freesurfer/dev/bin/recon-all -skullstrip -gcut -s good_output/ subjid good_output setenv SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /usr/local/freesurfer/dev Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/dev build-stamp.txt: freesurfer-Linux-centos4_x86_64-dev-20110425 Linux dharma 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 137216 total used free shared buffers cached Mem: 16438368 15300692 1137676 0 303544 13277352 -/+ buffers/cache: 1719796 14718572 Swap: 16386260 0 16386260 ######################################## program versions used $Id: recon-all,v 1.386 2011/03/30 21:59:00 mreuter Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:15-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:16-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: tkregister2.c,v 1.122 2011/03/28 20:24:46 greve Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:17-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:18-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:18-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:19-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:20-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:20-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:21-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_em_register.c,v 1.89 2011/04/15 13:46:26 rge21 Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:22-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_ca_normalize.c,v 1.53 2011/04/14 13:00:23 fischl Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:23-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:23-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_ca_label.c,v 1.97 2011/04/14 11:36:06 fischl Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:24-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:25-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:25-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:26-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:27-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:27-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:28-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:29-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:29-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:30-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:31-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:32-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:32-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:33-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:34-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:34-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:35-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:36-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:36-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:37-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mris_calc.c,v 1.41 2011/04/04 00:20:44 rudolph Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:38-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:38-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:39-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:40-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:41-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2011/04/25-16:04:41-GMT BuildTimeStamp: Apr 25 2011 05:10:23 CVS: $Id: mri_segstats.c,v 1.76 2011/04/19 21:24:27 greve Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/dev/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/dev/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/dev Previous: /usr/local/freesurfer/stable5 #-------------------------------------------- #@# Skull Stripping Mon Apr 25 12:04:43 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /usr/local/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading extra input line fscale 0.150000 freadFloat: fread failed ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz freadFloat: fread failed freadFloat: fread failed Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=103 z=122 r=81 first estimation of the main basin volume: 2305775 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=108, y=88, z=83, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=906013759793059 voxels, voxel volume =1.000 = 906013759793059 mmm3 = 906013754523.648 cm3 done. PostAnalyze...Basin Prior 72 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=109, z=114, r=10066 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=39 , nb = 45108 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=22 , nb = 2898 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=21 , nb = 2754 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = 19404 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=39 , nb = 19314 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=68 , nb = 738 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 32, 26, 58 after analyzing : 26, 32, 32, 38 RIGHT_CER before analyzing : 22, 29, 39, 66 after analyzing : 22, 35, 39, 42 LEFT_CER before analyzing : 21, 26, 36, 68 after analyzing : 21, 32, 36, 41 RIGHT_BRAIN before analyzing : 40, 32, 24, 58 after analyzing : 26, 32, 32, 38 LEFT_BRAIN before analyzing : 39, 32, 25, 58 after analyzing : 26, 32, 32, 38 OTHER before analyzing : 68, 77, 80, 95 after analyzing : 68, 79, 80, 83 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 68.510, std = 8.304 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.83, sigma = 4.28 after rotation: sse = 2.83, sigma = 4.28 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.90, its var is 3.76 before Erosion-Dilatation 0.29% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations freadFloat: fread failed mri_strip_skull: done peeling brain Brain Size = 1541610 voxels, voxel volume = 1.000 mm3 = 1541610 mmm3 = 1541.610 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done rm -f brainmask.gcuts.mgz mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed. freadFloat: fread failed reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.400000=44.000000 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... mri_binarize --i brainmask.gcuts.mgz --o brainmask.gcuts.mgz --binval 999 --min 1 $Id: mri_binarize.c,v 1.27 2011/04/08 15:40:27 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri cmdline mri_binarize --i brainmask.gcuts.mgz --o brainmask.gcuts.mgz --binval 999 --min 1 sysname Linux hostname dharma machine x86_64 user khoa input brainmask.gcuts.mgz frame 0 nErode3d 0 nErode2d 0 output brainmask.gcuts.mgz Binarizing based on threshold min 1 max +infinity binval 999 binvalnot 0 Found 153211 values in range Counting number of voxels Found 153211 voxels in final mask mri_binarize done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------------ recon-all -s good_output finished without error at Mon Apr 25 12:05:55 EDT 2011 New invocation of recon-all Thu May 19 19:05:11 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output /space/freesurfer/centos4.0_x86_64/stable5/bin/recon-all -all -clean -s good_output/ subjid good_output setenv SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110519 Linux compute-0-2.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse 4194304 kbytes vmemoryuse 8388608 kbytes descriptors 4096 memorylocked 4194304 kbytes maxproc 268288 total used free shared buffers cached Mem: 32962780 11008204 21954576 0 153460 3812076 -/+ buffers/cache: 7042668 25920112 Swap: 32764556 8596756 24167800 ######################################## program versions used $Id: recon-all,v 1.379.2.16 2011/05/18 23:02:13 krish Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:12-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:12-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:14-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:14-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:15-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:15-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:15-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:15-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:16-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:16-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:17-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:17-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:17-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:17-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:18-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:18-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:18-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:18-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:19-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:19-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:19-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:19-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:20-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:20-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:20-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:20-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:21-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:21-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:21-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:22-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:22-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:22-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:23-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:23-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:23-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:23-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:24-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/19-23:05:24-GMT BuildTimeStamp: May 19 2011 13:16:57 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: khoa Machine: compute-0-2.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /space/freesurfer/centos4.0_x86_64/stable5/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /space/freesurfer/centos4.0_x86_64/stable5/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts/seed-*.crs.man.dat /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: No match. mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/tmp/cw256 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/tmp/cw256': No such file or directory mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/talairach.xfm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/*.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/optimal_preflood_height /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/optimal_preflood_height': No such file or directory mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/optimal_skullstrip_invol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/optimal_skullstrip_invol': No such file or directory mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brainmask.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.manedit.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.manedit.mgz': No such file or directory mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.seg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/tmp/control.dat /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/tmp/control.dat': No such file or directory mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.manedit.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.manedit.mgz': No such file or directory mv -f /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts/expert-options /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/trash mv: cannot stat `/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts/expert-options': No such file or directory #-------------------------------------------- #@# MotionCor Thu May 19 19:05:26 EDT 2011 Found 4 runs /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_robust_template --mov /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006.mgz --average 1 --template /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003-iscale.txt /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004-iscale.txt /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005-iscale.txt /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006-iscale.txt --subsample 200 --lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005.lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz as movable/source volume. --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004.mgz as movable/source volume. --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005.mgz as movable/source volume. --mov: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006.mgz as movable/source volume. Total: 4 input volumes --average: Using method 1 for template computation. --template: Using /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz'... reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004.mgz'... reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005.mgz'... reading source '/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/004.mgz ) to TP 1 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0510677 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.134992 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.289835 ), max sat: 8 ( 0.134992 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 6 ( 0.198691 ), max sat: 8 ( 0.134992 ), sat diff: 2 -- Iteration: 5 trying sat: 7 min sat: 6 ( 0.198691 ), max sat: 7 ( 0.161416 ), sat diff: 1 -- Iteration: 6 trying sat: 6.5 - final SAT: 7 ( it: 6 , weight check 0.161416 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.2343023547553 0 1.0000000000000 0 1.9495317750505 0 0 1.0000000000000 -1.0355476336448 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 0.294883 Iteration(f): 2 -- diff. to prev. transform: 0.240949 Iteration(f): 3 -- diff. to prev. transform: 0.201137 Iteration(f): 4 -- diff. to prev. transform: 0.255175 Iteration(f): 5 -- diff. to prev. transform: 0.273283 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 0.62108 Iteration(f): 2 -- diff. to prev. transform: 0.12048 Iteration(f): 3 -- diff. to prev. transform: 0.0154686 Iteration(f): 4 -- diff. to prev. transform: 0.0284834 Iteration(f): 5 -- diff. to prev. transform: 0.0205718 max it: 5 reached! Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.25473 Iteration(f): 2 -- diff. to prev. transform: 0.0415062 Iteration(f): 3 -- diff. to prev. transform: 0.0060009 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.037654 Iteration(f): 2 -- diff. to prev. transform: 0.00305546 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.0572993 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00233612 < 0.01 :-) - final transform: Tf = [ ... 0.9999952532724 0.0030807619812 -0.0000483559178 -0.3593856351262 -0.0030808431754 0.9999936700650 -0.0017799537137 0.8939839744116 0.0000428719980 0.0017800942417 0.9999984147120 -0.1344765713439 0 0 0 1.0000000000000 ] - final iscale: If = 1.00741 [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/005.mgz ) to TP 1 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0459896 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.121093 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.270528 ), max sat: 8 ( 0.121093 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 4 ( 0.270528 ), max sat: 6 ( 0.171163 ), sat diff: 2 -- Iteration: 5 trying sat: 5 min sat: 5 ( 0.212132 ), max sat: 6 ( 0.171163 ), sat diff: 1 -- Iteration: 6 trying sat: 5.5 - final SAT: 6 ( it: 6 , weight check 0.171163 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 0.0806232774706 0 1.0000000000000 0 -0.8587878652708 0 0 1.0000000000000 0.2893228397368 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 0.693533 Iteration(f): 2 -- diff. to prev. transform: 0.356665 Iteration(f): 3 -- diff. to prev. transform: 0.221343 Iteration(f): 4 -- diff. to prev. transform: 0.0790383 Iteration(f): 5 -- diff. to prev. transform: 0.0497159 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 0.627751 Iteration(f): 2 -- diff. to prev. transform: 0.071911 Iteration(f): 3 -- diff. to prev. transform: 0.0207046 Iteration(f): 4 -- diff. to prev. transform: 0.0224564 Iteration(f): 5 -- diff. to prev. transform: 0.00352928 < 0.01 :-) Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.0924509 Iteration(f): 2 -- diff. to prev. transform: 0.0040507 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.0510274 Iteration(f): 2 -- diff. to prev. transform: 0.00223367 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.0745268 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00101638 < 0.01 :-) - final transform: Tf = [ ... 0.9999802186722 0.0062650551716 -0.0005579857407 -0.6093224297684 -0.0062675520081 0.9999698178567 -0.0045914232603 1.5307222443389 0.0005292033795 0.0045948296405 0.9999893036850 -0.4733785840426 0 0 0 1.0000000000000 ] - final iscale: If = 0.995414 [init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/006.mgz ) to TP 1 ( /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig/003.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0440043 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.11956 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.266169 ), max sat: 8 ( 0.11956 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 4 ( 0.266169 ), max sat: 6 ( 0.169667 ), sat diff: 2 -- Iteration: 5 trying sat: 5 min sat: 5 ( 0.209271 ), max sat: 6 ( 0.169667 ), sat diff: 1 -- Iteration: 6 trying sat: 5.5 - final SAT: 6 ( it: 6 , weight check 0.169667 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 0.3738766040319 0 1.0000000000000 0 -1.0419889793102 0 0 1.0000000000000 -0.1815358958855 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 0.870795 Iteration(f): 2 -- diff. to prev. transform: 0.475828 Iteration(f): 3 -- diff. to prev. transform: 0.702409 Iteration(f): 4 -- diff. to prev. transform: 0.460156 Iteration(f): 5 -- diff. to prev. transform: 0.254227 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 0.583628 Iteration(f): 2 -- diff. to prev. transform: 0.0611544 Iteration(f): 3 -- diff. to prev. transform: 0.0218413 Iteration(f): 4 -- diff. to prev. transform: 0.00882035 < 0.01 :-) Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.0665332 Iteration(f): 2 -- diff. to prev. transform: 0.00941424 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.167613 Iteration(f): 2 -- diff. to prev. transform: 0.00753165 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.131601 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00326723 < 0.01 :-) - final transform: Tf = [ ... 0.9999916172533 0.0040559314020 -0.0005611092504 -0.2904089323400 -0.0040567874893 0.9999905960353 -0.0015330740971 1.1135515952652 0.0005548859304 0.0015353375467 0.9999986674192 -0.0809349067904 0 0 0 1.0000000000000 ] - final iscale: If = 0.993285 warping movs and creating initial template... allow intensity scaling using median Writing final template: /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 Determinant( lta[ 3 ]) : 1 registration took 2 minutes and 37 seconds. /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_convert /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/rawavg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig.mgz --conform mri_convert /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/rawavg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/talairach.xfm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 19 19:08:17 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu May 19 19:09:18 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7938, pval=0.8469 >= threshold=0.0050) awk -f /space/freesurfer/centos4.0_x86_64/stable5/bin/extract_talairach_avi_QA.awk /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/talairach_avi.log TalAviQA: 0.97980 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu May 19 19:09:19 EDT 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri /space/freesurfer/centos4.0_x86_64/stable5/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux compute-0-2.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux Thu May 19 19:09:20 EDT 2011 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.30478 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30478/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30478/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30478/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu May 19 19:09:27 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.30478/nu0.mnc ./tmp.mri_nu_correct.mni.30478/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30478/0/ [khoa@compute-0-2.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/] [2011-05-19 19:09:29] running: /space/freesurfer/centos4.0_x86_64/stable5/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.30478/0/ ./tmp.mri_nu_correct.mni.30478/nu0.mnc ./tmp.mri_nu_correct.mni.30478/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 28 CV of field change: 0.000996719 [khoa@compute-0-2.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/] [2011-05-19 19:10:36] running: /space/freesurfer/centos4.0_x86_64/stable5/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.30478/nu0.mnc ./tmp.mri_nu_correct.mni.30478/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu May 19 19:10:53 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.30478/nu1.mnc ./tmp.mri_nu_correct.mni.30478/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.30478/1/ [khoa@compute-0-2.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/] [2011-05-19 19:10:55] running: /space/freesurfer/centos4.0_x86_64/stable5/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.30478/1/ ./tmp.mri_nu_correct.mni.30478/nu1.mnc ./tmp.mri_nu_correct.mni.30478/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000983558 [khoa@compute-0-2.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/] [2011-05-19 19:12:01] running: /space/freesurfer/centos4.0_x86_64/stable5/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.30478/nu1.mnc ./tmp.mri_nu_correct.mni.30478/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.30478/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.30478/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.30478/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.30478/ones.mgz sysname Linux hostname compute-0-2.local machine x86_64 user khoa input ./tmp.mri_nu_correct.mni.30478/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.30478/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30478/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.30478/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30478/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30478/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.30478/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30478/input.mean.dat sysname Linux hostname compute-0-2.local machine x86_64 user khoa Loading ./tmp.mri_nu_correct.mni.30478/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.30478/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30478/ones.mgz --i ./tmp.mri_nu_correct.mni.30478/nu2.mnc --sum ./tmp.mri_nu_correct.mni.30478/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30478/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30478/ones.mgz --i ./tmp.mri_nu_correct.mni.30478/nu2.mnc --sum ./tmp.mri_nu_correct.mni.30478/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30478/output.mean.dat sysname Linux hostname compute-0-2.local machine x86_64 user khoa Loading ./tmp.mri_nu_correct.mni.30478/ones.mgz Loading ./tmp.mri_nu_correct.mni.30478/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.30478/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.30478/nu2.mnc ./tmp.mri_nu_correct.mni.30478/nu2.mnc mul 1.05068900363734836688 Saving result to './tmp.mri_nu_correct.mni.30478/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.30478/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.30478/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.30478/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 12 seconds. mapping (13, 126) to ( 3, 110) Thu May 19 19:14:01 EDT 2011 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Thu May 19 19:14:01 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.085 0.011 -0.012 0.419; -0.036 1.010 0.133 -12.315; 0.008 -0.072 1.165 -14.962; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 17 seconds. MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 white matter peak found at 111 white matter peak found at 108 gm peak at 56 (56), valley at 34 (34) csf peak at 28, setting threshold to 46 white matter peak found at 111 white matter peak found at 110 gm peak at 59 (59), valley at 33 (33) csf peak at 30, setting threshold to 49 #-------------------------------------------- #@# Skull Stripping Thu May 19 19:16:20 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_em_register -skull nu.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (50, 30, 19) --> (205, 238, 223) using (102, 99, 121) as brain centroid... mean wm in atlas = 126, using box (83,73,96) --> (121, 124,146) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 initial log_p = -10407.5 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.3, 4.8, -9.4): log p = -10319.262 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10318.4, old_max_log_p =-10319.3 (thresh=-10308.9) 1.075 0.000 0.000 -9.737; 0.000 1.075 0.000 -3.892; 0.000 0.000 1.000 -9.375; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10298.3, old_max_log_p =-10318.4 (thresh=-10308.0) 1.094 -0.002 0.033 -17.711; 0.000 1.134 0.067 -14.917; -0.037 -0.071 1.035 -2.586; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10279.2, old_max_log_p =-10298.3 (thresh=-10288.0) 1.114 0.034 -0.001 -20.243; -0.034 1.200 0.034 -12.156; -0.002 -0.034 1.018 -9.204; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10273.5, old_max_log_p =-10279.2 (thresh=-10268.9) 1.093 -0.005 -0.002 -13.150; 0.002 1.223 0.034 -19.448; -0.002 -0.034 1.018 -9.204; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10268.7, old_max_log_p =-10273.5 (thresh=-10263.2) 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 10268.7 tol 0.000010 Resulting transform: 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10268.7 (old=-10407.5) transform before final EM align: 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09425 -0.02462 -0.01915 -9.08565; 0.02029 1.21825 0.03376 -21.16974; 0.01575 -0.03414 1.01389 -11.04904; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1144141.8 tol 0.000000 final transform: 1.094 -0.025 -0.019 -9.086; 0.020 1.218 0.034 -21.170; 0.016 -0.034 1.014 -11.049; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 23 minutes and 18 seconds. mri_watershed -T1 -brain_atlas /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=103 z=121 r=81 first estimation of the main basin volume: 2299224 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=109, y=86, z=84, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=30600491099 voxels, voxel volume =1.000 = 30600491099 mmm3 = 30600491.008 cm3 done. PostAnalyze...Basin Prior 112 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=110, z=114, r=10061 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 44532 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=19 , nb = 2682 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=14 , nb = 2502 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = 19548 LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 19206 OTHER CSF_MIN=0, CSF_intensity=13, CSF_MAX=44 , nb = 594 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 31, 23, 58 after analyzing : 24, 31, 31, 37 RIGHT_CER before analyzing : 19, 26, 39, 68 after analyzing : 19, 34, 39, 42 LEFT_CER before analyzing : 14, 17, 29, 66 after analyzing : 14, 25, 29, 35 RIGHT_BRAIN before analyzing : 40, 31, 22, 58 after analyzing : 25, 31, 31, 37 LEFT_BRAIN before analyzing : 39, 31, 23, 58 after analyzing : 24, 31, 31, 37 OTHER before analyzing : 44, 72, 83, 95 after analyzing : 44, 79, 83, 83 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 68.965, std = 8.022 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.46, sigma = 3.66 after rotation: sse = 2.46, sigma = 3.66 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.50, its var is 3.14 before Erosion-Dilatation 0.11% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...49 iterations mri_strip_skull: done peeling brain Brain Size = 1565708 voxels, voxel volume = 1.000 mm3 = 1565708 mmm3 = 1565.708 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu May 19 19:40:22 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (61, 50, 36) --> (194, 162, 203) using (105, 87, 120) as brain centroid... mean wm in atlas = 107, using box (89,73,99) --> (121, 100,140) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -7444.2 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, 8.5, -8.5): log p = -7126.301 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6999.5, old_max_log_p =-7126.3 (thresh=-7119.2) 1.064 0.000 0.000 -8.688; 0.000 1.226 0.140 -32.353; 0.000 -0.150 0.991 9.014; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6999.5, old_max_log_p =-6999.5 (thresh=-6992.5) 1.064 0.000 0.000 -8.688; 0.000 1.226 0.140 -32.353; 0.000 -0.150 0.991 9.014; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6900.3, old_max_log_p =-6999.5 (thresh=-6992.5) 1.043 0.000 0.000 -7.998; 0.000 1.256 0.077 -28.441; 0.000 -0.068 0.980 -2.362; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6883.1, old_max_log_p =-6900.3 (thresh=-6893.4) 1.062 0.000 0.000 -10.431; 0.000 1.253 0.109 -30.011; 0.000 -0.111 0.995 2.463; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6883.1, old_max_log_p =-6883.1 (thresh=-6876.3) 1.062 0.000 0.000 -10.431; 0.000 1.253 0.109 -30.011; 0.000 -0.111 0.995 2.463; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6848.1, old_max_log_p =-6883.1 (thresh=-6876.3) 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6848.1, old_max_log_p =-6848.1 (thresh=-6841.2) 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 6847.1 after pass:transform: ( 1.06, -0.03, -0.01, -6.23) ( 0.03, 1.25, 0.09, -31.93) ( 0.01, -0.09, 1.00, -0.92) dfp_em_step_func: 009: -log(p) = 6846.1 after pass:transform: ( 1.06, -0.03, -0.01, -6.23) ( 0.03, 1.25, 0.09, -31.93) ( 0.01, -0.09, 1.00, -0.92) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 6846.1 tol 0.000010 Resulting transform: 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -6848.1 (old=-7444.2) transform before final EM align: 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 012: -log(p) = 832565.0 after pass:transform: ( 1.06, -0.03, -0.01, -6.23) ( 0.03, 1.25, 0.09, -31.93) ( 0.01, -0.09, 1.00, -0.92) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 832565.0 tol 0.000000 final transform: 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 25 minutes and 36 seconds. #-------------------------------------- #@# CA Normalize Thu May 19 20:05:58 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (61, 50, 37) --> (194, 162, 203) using (105, 87, 120) as brain centroid... mean wm in atlas = 107, using box (89,73,100) --> (121, 100,140) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (191, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 236.0 0 of 46 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (129, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 236.0 0 of 84 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (176, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 236.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 123, 59) --> (129, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 236.0 1 of 10 (10.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 118, 96) --> (145, 173, 127) Brain_Stem: limiting intensities to 87.0 --> 236.0 0 of 6 (0.0%) samples deleted using 157 total control points for intensity normalization... bias field = 0.995 +- 0.063 0 of 156 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (191, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 213.0 0 of 105 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (129, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 213.0 0 of 111 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (176, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 213.0 0 of 22 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 123, 59) --> (129, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 213.0 0 of 56 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 118, 96) --> (145, 173, 127) Brain_Stem: limiting intensities to 67.0 --> 213.0 0 of 82 (0.0%) samples deleted using 376 total control points for intensity normalization... bias field = 0.996 +- 0.044 0 of 376 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (191, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 210.0 0 of 219 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (129, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 210.0 0 of 263 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (176, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 210.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 123, 59) --> (129, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 210.0 0 of 48 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 118, 96) --> (145, 173, 127) Brain_Stem: limiting intensities to 80.0 --> 210.0 29 of 136 (21.3%) samples deleted using 751 total control points for intensity normalization... bias field = 0.995 +- 0.038 0 of 722 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 58 seconds. #-------------------------------------- #@# CA Reg Thu May 19 20:07:57 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.34 (predicted orig area = 6.0) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.905, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53785.660 ms 0001: dt=129.472000, rms=0.852 (5.851%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52890.781 ms 0002: dt=129.472000, rms=0.820 (3.748%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62651.883 ms 0003: dt=92.480000, rms=0.815 (0.646%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69177.336 ms 0004: dt=369.920000, rms=0.794 (2.528%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65065.523 ms 0005: dt=32.368000, rms=0.791 (0.427%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66462.797 ms 0006: dt=32.368000, rms=0.790 (0.156%), neg=0, invalid=766 0007: dt=32.368000, rms=0.789 (0.096%), neg=0, invalid=766 0008: dt=32.368000, rms=0.788 (0.116%), neg=0, invalid=766 0009: dt=32.368000, rms=0.787 (0.154%), neg=0, invalid=766 0010: dt=32.368000, rms=0.785 (0.273%), neg=0, invalid=766 0011: dt=32.368000, rms=0.781 (0.420%), neg=0, invalid=766 0012: dt=32.368000, rms=0.778 (0.488%), neg=0, invalid=766 0013: dt=32.368000, rms=0.774 (0.462%), neg=0, invalid=766 0014: dt=32.368000, rms=0.771 (0.405%), neg=0, invalid=766 0015: dt=32.368000, rms=0.768 (0.345%), neg=0, invalid=766 0016: dt=32.368000, rms=0.766 (0.272%), neg=0, invalid=766 0017: dt=32.368000, rms=0.764 (0.229%), neg=0, invalid=766 0018: dt=32.368000, rms=0.762 (0.248%), neg=0, invalid=766 0019: dt=32.368000, rms=0.760 (0.316%), neg=0, invalid=766 0020: dt=32.368000, rms=0.757 (0.361%), neg=0, invalid=766 0021: dt=32.368000, rms=0.755 (0.352%), neg=0, invalid=766 0022: dt=32.368000, rms=0.752 (0.304%), neg=0, invalid=766 0023: dt=32.368000, rms=0.751 (0.245%), neg=0, invalid=766 0024: dt=32.368000, rms=0.749 (0.205%), neg=0, invalid=766 0025: dt=32.368000, rms=0.748 (0.174%), neg=0, invalid=766 0026: dt=32.368000, rms=0.746 (0.204%), neg=0, invalid=766 0027: dt=32.368000, rms=0.744 (0.254%), neg=0, invalid=766 0028: dt=32.368000, rms=0.742 (0.285%), neg=0, invalid=766 0029: dt=32.368000, rms=0.740 (0.282%), neg=0, invalid=766 0030: dt=32.368000, rms=0.738 (0.246%), neg=0, invalid=766 0031: dt=32.368000, rms=0.737 (0.209%), neg=0, invalid=766 0032: dt=32.368000, rms=0.735 (0.167%), neg=0, invalid=766 0033: dt=32.368000, rms=0.734 (0.147%), neg=0, invalid=766 0034: dt=32.368000, rms=0.733 (0.156%), neg=0, invalid=766 0035: dt=32.368000, rms=0.732 (0.178%), neg=0, invalid=766 0036: dt=32.368000, rms=0.730 (0.213%), neg=0, invalid=766 0037: dt=32.368000, rms=0.729 (0.214%), neg=0, invalid=766 0038: dt=32.368000, rms=0.727 (0.195%), neg=0, invalid=766 0039: dt=32.368000, rms=0.726 (0.169%), neg=0, invalid=766 0040: dt=32.368000, rms=0.725 (0.143%), neg=0, invalid=766 0041: dt=32.368000, rms=0.724 (0.121%), neg=0, invalid=766 0042: dt=32.368000, rms=0.723 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70444.812 ms 0043: dt=1183.744000, rms=0.720 (0.474%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64583.453 ms 0044: dt=27.744000, rms=0.719 (0.088%), neg=0, invalid=766 0045: dt=27.744000, rms=0.719 (0.011%), neg=0, invalid=766 0046: dt=27.744000, rms=0.719 (-0.125%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50520.375 ms 0047: dt=4.624000, rms=0.719 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65054.719 ms 0048: dt=4.624000, rms=0.719 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84274.125 ms 0049: dt=0.000181, rms=0.719 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.725, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60775.660 ms 0050: dt=145.152000, rms=0.703 (3.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63854.012 ms 0051: dt=62.208000, rms=0.685 (2.540%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63244.297 ms 0052: dt=13.636364, rms=0.683 (0.269%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54500.480 ms 0053: dt=36.288000, rms=0.681 (0.351%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53669.395 ms 0054: dt=145.152000, rms=0.669 (1.724%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58368.406 ms 0055: dt=9.072000, rms=0.667 (0.347%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69894.070 ms 0056: dt=9.523810, rms=0.666 (0.173%), neg=0, invalid=766 0057: dt=9.523810, rms=0.665 (0.086%), neg=0, invalid=766 0058: dt=9.523810, rms=0.664 (0.105%), neg=0, invalid=766 0059: dt=9.523810, rms=0.663 (0.151%), neg=0, invalid=766 0060: dt=9.523810, rms=0.662 (0.268%), neg=0, invalid=766 0061: dt=9.523810, rms=0.659 (0.401%), neg=0, invalid=766 0062: dt=9.523810, rms=0.656 (0.468%), neg=0, invalid=766 0063: dt=9.523810, rms=0.653 (0.451%), neg=0, invalid=766 0064: dt=9.523810, rms=0.650 (0.416%), neg=0, invalid=766 0065: dt=9.523810, rms=0.648 (0.391%), neg=0, invalid=766 0066: dt=9.523810, rms=0.645 (0.365%), neg=0, invalid=766 0067: dt=9.523810, rms=0.643 (0.329%), neg=0, invalid=766 0068: dt=9.523810, rms=0.641 (0.321%), neg=0, invalid=766 0069: dt=9.523810, rms=0.639 (0.356%), neg=0, invalid=766 0070: dt=9.523810, rms=0.636 (0.383%), neg=0, invalid=766 0071: dt=9.523810, rms=0.634 (0.373%), neg=0, invalid=766 0072: dt=9.523810, rms=0.632 (0.337%), neg=0, invalid=766 0073: dt=9.523810, rms=0.630 (0.290%), neg=0, invalid=766 0074: dt=9.523810, rms=0.628 (0.254%), neg=0, invalid=766 0075: dt=9.523810, rms=0.627 (0.226%), neg=0, invalid=766 0076: dt=9.523810, rms=0.626 (0.200%), neg=0, invalid=766 0077: dt=9.523810, rms=0.625 (0.194%), neg=0, invalid=766 0078: dt=9.523810, rms=0.623 (0.201%), neg=0, invalid=766 0079: dt=9.523810, rms=0.622 (0.211%), neg=0, invalid=766 0080: dt=9.523810, rms=0.621 (0.193%), neg=0, invalid=766 0081: dt=9.523810, rms=0.620 (0.171%), neg=0, invalid=766 0082: dt=9.523810, rms=0.619 (0.145%), neg=0, invalid=766 0083: dt=9.523810, rms=0.618 (0.127%), neg=0, invalid=766 0084: dt=9.523810, rms=0.617 (0.109%), neg=0, invalid=766 0085: dt=9.523810, rms=0.617 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73392.000 ms 0086: dt=145.152000, rms=0.616 (0.166%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58752.289 ms 0087: dt=9.072000, rms=0.616 (0.007%), neg=0, invalid=766 0088: dt=9.072000, rms=0.616 (0.005%), neg=0, invalid=766 0089: dt=9.072000, rms=0.616 (-0.009%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59846.707 ms 0090: dt=9.072000, rms=0.616 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69061.797 ms 0091: dt=9.072000, rms=0.616 (0.008%), neg=0, invalid=766 0092: dt=9.072000, rms=0.615 (0.007%), neg=0, invalid=766 0093: dt=9.072000, rms=0.615 (0.001%), neg=0, invalid=766 0094: dt=9.072000, rms=0.615 (-0.008%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70033.414 ms 0095: dt=5.250000, rms=0.643 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78356.828 ms 0096: dt=2.000000, rms=0.643 (0.008%), neg=0, invalid=766 0097: dt=2.000000, rms=0.643 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.643, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69026.484 ms 0098: dt=0.000000, rms=0.643 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.720, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63171.949 ms 0099: dt=4.675900, rms=0.705 (2.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68660.188 ms 0100: dt=1.931818, rms=0.705 (0.087%), neg=0, invalid=766 0101: dt=1.931818, rms=0.705 (-0.034%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68648.422 ms 0102: dt=0.000000, rms=0.705 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.794, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52622.418 ms 0103: dt=0.994059, rms=0.790 (0.474%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75598.234 ms 0104: dt=1.792000, rms=0.785 (0.622%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59703.531 ms 0105: dt=0.940171, rms=0.785 (0.103%), neg=0, invalid=766 0106: dt=0.940171, rms=0.784 (0.089%), neg=0, invalid=766 0107: dt=0.940171, rms=0.784 (-0.030%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.784, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71772.117 ms 0108: dt=1.383178, rms=0.782 (0.189%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66155.461 ms 0109: dt=0.000000, rms=0.782 (-0.003%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.717, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70225.773 ms 0110: dt=0.448000, rms=0.694 (3.216%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57841.449 ms 0111: dt=0.000000, rms=0.694 (0.011%), neg=0, invalid=766 0112: dt=0.050000, rms=0.694 (-0.427%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58398.441 ms 0113: dt=0.000000, rms=0.694 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.17736 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (2202 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2202 voxels, peak = 4), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.11250 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (1889 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1889 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.10366 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (324 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (324 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.08467 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, overlap=0.998) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, peak = 97), gca=97.0 gca peak = 0.24007 (63) mri peak = 0.07136 (58) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (547 voxels, overlap=0.930) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (547 voxels, peak = 58), gca=58.3 gca peak = 0.29892 (64) mri peak = 0.07486 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (547 voxels, overlap=0.960) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (547 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.08462 (107) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (56773 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (56773 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.07394 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (59084 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (59084 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03685 (60) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (18786 voxels, overlap=0.711) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (18786 voxels, peak = 57), gca=56.7 gca peak = 0.13270 (63) mri peak = 0.03245 (63) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (19623 voxels, overlap=0.506) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (19623 voxels, peak = 60), gca=59.8 gca peak = 0.15182 (70) mri peak = 0.07620 (64) Right_Caudate (50): linear fit = 0.88 x + 0.0 (325 voxels, overlap=0.006) Right_Caudate (50): linear fit = 0.88 x + 0.0 (325 voxels, peak = 61), gca=61.2 gca peak = 0.14251 (76) mri peak = 0.08822 (70) Left_Caudate (11): linear fit = 0.85 x + 0.0 (790 voxels, overlap=0.325) Left_Caudate (11): linear fit = 0.85 x + 0.0 (790 voxels, peak = 65), gca=64.6 gca peak = 0.12116 (60) mri peak = 0.03810 (57) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (22307 voxels, overlap=0.842) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (22307 voxels, peak = 57), gca=57.0 gca peak = 0.12723 (61) mri peak = 0.04199 (55) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (25928 voxels, overlap=0.843) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (25928 voxels, peak = 58), gca=58.0 gca peak = 0.22684 (88) mri peak = 0.07970 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7062 voxels, overlap=0.581) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7062 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.08025 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6914 voxels, overlap=0.617) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6914 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.11437 (56) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, overlap=0.832) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.12892 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (311 voxels, overlap=0.931) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (311 voxels, peak = 56), gca=55.8 gca peak = 0.10129 (93) mri peak = 0.05147 (90) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4627 voxels, overlap=0.899) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4627 voxels, peak = 91), gca=90.7 gca peak = 0.12071 (89) mri peak = 0.06659 (84) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3304 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3304 voxels, peak = 87), gca=86.8 gca peak = 0.13716 (82) mri peak = 0.05625 (79) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2119 voxels, overlap=0.662) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2119 voxels, peak = 76), gca=75.8 gca peak = 0.15214 (84) mri peak = 0.04259 (83) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2306 voxels, overlap=0.711) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2306 voxels, peak = 80), gca=79.8 gca peak = 0.08983 (85) mri peak = 0.06377 (85) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10520 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10520 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.09287 (101) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (876 voxels, overlap=0.590) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (876 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.10302 (100) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1092 voxels, overlap=0.757) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1092 voxels, peak = 99), gca=98.7 gca peak = 0.21100 (36) mri peak = 0.11115 ( 5) gca peak = 0.13542 (27) mri peak = 0.16850 ( 8) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (409 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (409 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.716, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63762.258 ms 0114: dt=129.472000, rms=0.708 (1.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66567.945 ms 0115: dt=221.952000, rms=0.703 (0.780%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45506.039 ms 0116: dt=32.368000, rms=0.702 (0.143%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43260.582 ms 0117: dt=92.480000, rms=0.701 (0.130%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48370.730 ms 0118: dt=369.920000, rms=0.698 (0.472%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42891.047 ms 0119: dt=32.368000, rms=0.697 (0.143%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46518.004 ms 0120: dt=32.368000, rms=0.696 (0.035%), neg=0, invalid=766 0121: dt=32.368000, rms=0.696 (0.020%), neg=0, invalid=766 0122: dt=32.368000, rms=0.696 (0.044%), neg=0, invalid=766 0123: dt=32.368000, rms=0.695 (0.064%), neg=0, invalid=766 0124: dt=32.368000, rms=0.695 (0.108%), neg=0, invalid=766 0125: dt=32.368000, rms=0.694 (0.138%), neg=0, invalid=766 0126: dt=32.368000, rms=0.693 (0.143%), neg=0, invalid=766 0127: dt=32.368000, rms=0.692 (0.127%), neg=0, invalid=766 0128: dt=32.368000, rms=0.691 (0.115%), neg=0, invalid=766 0129: dt=32.368000, rms=0.690 (0.110%), neg=0, invalid=766 0130: dt=32.368000, rms=0.689 (0.119%), neg=0, invalid=766 0131: dt=32.368000, rms=0.689 (0.126%), neg=0, invalid=766 0132: dt=32.368000, rms=0.688 (0.128%), neg=0, invalid=766 0133: dt=32.368000, rms=0.687 (0.126%), neg=0, invalid=766 0134: dt=32.368000, rms=0.686 (0.117%), neg=0, invalid=766 0135: dt=32.368000, rms=0.685 (0.105%), neg=0, invalid=766 0136: dt=32.368000, rms=0.685 (0.098%), neg=0, invalid=766 0137: dt=32.368000, rms=0.684 (0.095%), neg=0, invalid=766 0138: dt=32.368000, rms=0.683 (0.097%), neg=0, invalid=766 0139: dt=32.368000, rms=0.683 (0.100%), neg=0, invalid=766 0140: dt=32.368000, rms=0.682 (0.106%), neg=0, invalid=766 0141: dt=32.368000, rms=0.681 (0.099%), neg=0, invalid=766 0142: dt=32.368000, rms=0.681 (0.093%), neg=0, invalid=766 0143: dt=32.368000, rms=0.680 (0.085%), neg=0, invalid=766 0144: dt=32.368000, rms=0.679 (0.077%), neg=0, invalid=766 0145: dt=32.368000, rms=0.679 (0.080%), neg=0, invalid=766 0146: dt=32.368000, rms=0.678 (0.077%), neg=0, invalid=766 0147: dt=32.368000, rms=0.678 (0.083%), neg=0, invalid=766 0148: dt=32.368000, rms=0.677 (0.083%), neg=0, invalid=766 0149: dt=32.368000, rms=0.677 (0.081%), neg=0, invalid=766 0150: dt=32.368000, rms=0.676 (0.074%), neg=0, invalid=766 0151: dt=32.368000, rms=0.676 (0.072%), neg=0, invalid=766 0152: dt=32.368000, rms=0.675 (0.066%), neg=0, invalid=766 0153: dt=32.368000, rms=0.675 (0.070%), neg=0, invalid=766 0154: dt=32.368000, rms=0.674 (0.072%), neg=0, invalid=766 0155: dt=32.368000, rms=0.674 (0.072%), neg=0, invalid=766 0156: dt=32.368000, rms=0.673 (0.070%), neg=0, invalid=766 0157: dt=32.368000, rms=0.673 (0.067%), neg=0, invalid=766 0158: dt=32.368000, rms=0.673 (0.061%), neg=0, invalid=766 0159: dt=32.368000, rms=0.672 (0.055%), neg=0, invalid=766 0160: dt=32.368000, rms=0.672 (0.055%), neg=0, invalid=766 0161: dt=32.368000, rms=0.671 (0.063%), neg=0, invalid=766 0162: dt=32.368000, rms=0.671 (0.067%), neg=0, invalid=766 0163: dt=32.368000, rms=0.671 (0.059%), neg=0, invalid=766 0164: dt=32.368000, rms=0.670 (0.048%), neg=0, invalid=766 0165: dt=32.368000, rms=0.670 (0.042%), neg=0, invalid=766 0166: dt=32.368000, rms=0.670 (0.035%), neg=0, invalid=766 0167: dt=32.368000, rms=0.669 (0.047%), neg=0, invalid=766 0168: dt=32.368000, rms=0.669 (0.056%), neg=0, invalid=766 0169: dt=32.368000, rms=0.669 (0.049%), neg=0, invalid=766 0170: dt=32.368000, rms=0.668 (0.041%), neg=0, invalid=766 0171: dt=32.368000, rms=0.668 (0.034%), neg=0, invalid=766 0172: dt=32.368000, rms=0.668 (0.028%), neg=0, invalid=766 0173: dt=32.368000, rms=0.668 (0.039%), neg=0, invalid=766 0174: dt=32.368000, rms=0.667 (0.044%), neg=0, invalid=766 0175: dt=32.368000, rms=0.667 (0.049%), neg=0, invalid=766 0176: dt=32.368000, rms=0.667 (0.038%), neg=0, invalid=766 0177: dt=32.368000, rms=0.667 (0.027%), neg=0, invalid=766 0178: dt=32.368000, rms=0.667 (0.022%), neg=0, invalid=766 0179: dt=32.368000, rms=0.666 (0.034%), neg=0, invalid=766 0180: dt=32.368000, rms=0.666 (0.041%), neg=0, invalid=766 0181: dt=32.368000, rms=0.666 (0.049%), neg=0, invalid=766 0182: dt=32.368000, rms=0.665 (0.032%), neg=0, invalid=766 0183: dt=32.368000, rms=0.665 (0.023%), neg=0, invalid=766 0184: dt=32.368000, rms=0.665 (0.027%), neg=0, invalid=766 0185: dt=32.368000, rms=0.665 (0.030%), neg=0, invalid=766 0186: dt=32.368000, rms=0.665 (0.035%), neg=0, invalid=766 0187: dt=32.368000, rms=0.665 (0.024%), neg=0, invalid=766 0188: dt=32.368000, rms=0.664 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48383.918 ms 0189: dt=517.888000, rms=0.664 (0.104%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59896.793 ms 0190: dt=0.000542, rms=0.664 (-0.004%), neg=0, invalid=766 0191: dt=0.000542, rms=0.664 (0.000%), neg=0, invalid=766 0192: dt=0.000542, rms=0.664 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42368.211 ms 0193: dt=18.496000, rms=0.664 (0.014%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56328.117 ms 0194: dt=8.092000, rms=0.664 (0.002%), neg=0, invalid=766 0195: dt=8.092000, rms=0.664 (0.001%), neg=0, invalid=766 0196: dt=8.092000, rms=0.664 (0.002%), neg=0, invalid=766 0197: dt=8.092000, rms=0.664 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41354.934 ms 0198: dt=145.152000, rms=0.649 (2.374%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41331.676 ms 0199: dt=36.288000, rms=0.644 (0.765%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38363.477 ms 0200: dt=31.104000, rms=0.642 (0.248%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41689.953 ms 0201: dt=82.944000, rms=0.637 (0.799%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43537.492 ms 0202: dt=15.552000, rms=0.635 (0.358%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49957.562 ms 0203: dt=145.152000, rms=0.629 (0.816%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43666.793 ms 0204: dt=31.104000, rms=0.625 (0.641%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41326.668 ms 0205: dt=20.736000, rms=0.625 (0.123%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44967.473 ms 0206: dt=497.664000, rms=0.613 (1.807%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38067.301 ms 0207: dt=9.072000, rms=0.610 (0.549%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40968.816 ms 0208: dt=2.268000, rms=0.609 (0.100%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34194.137 ms 0209: dt=0.567000, rms=0.609 (0.018%), neg=0, invalid=766 0210: dt=0.283500, rms=0.609 (0.008%), neg=0, invalid=766 0211: dt=0.141750, rms=0.609 (0.004%), neg=0, invalid=766 0212: dt=0.035437, rms=0.609 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28655.150 ms 0213: dt=0.008859, rms=0.609 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30388.566 ms 0214: dt=0.008859, rms=0.609 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24931.117 ms 0215: dt=0.000000, rms=0.609 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.614, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21745.500 ms 0216: dt=0.000000, rms=0.614 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20509.367 ms 0217: dt=0.000000, rms=0.614 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.628, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49809.312 ms 0218: dt=0.000176, rms=0.628 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24191.014 ms 0219: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=766 0220: dt=0.000005, rms=0.628 (0.000%), neg=0, invalid=766 0221: dt=0.000001, rms=0.628 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.628, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21835.969 ms 0222: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.658, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48754.117 ms 0223: dt=0.448000, rms=0.651 (1.040%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50379.254 ms 0224: dt=0.448000, rms=0.645 (0.918%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46730.754 ms 0225: dt=0.448000, rms=0.640 (0.803%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42637.062 ms 0226: dt=0.448000, rms=0.635 (0.703%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46555.348 ms 0227: dt=1.792000, rms=0.620 (2.370%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46467.453 ms 0228: dt=1.792000, rms=0.612 (1.252%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46260.105 ms 0229: dt=1.792000, rms=0.608 (0.723%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43219.426 ms 0230: dt=0.448000, rms=0.607 (0.130%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46866.828 ms 0231: dt=1.792000, rms=0.604 (0.447%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47396.980 ms 0232: dt=1.792000, rms=0.603 (0.311%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49213.516 ms 0233: dt=1.280000, rms=0.602 (0.168%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48018.535 ms 0234: dt=0.525000, rms=0.601 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47967.145 ms 0235: dt=1.792000, rms=0.600 (0.188%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47642.781 ms 0236: dt=1.792000, rms=0.599 (0.151%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49702.457 ms 0237: dt=1.792000, rms=0.599 (0.118%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48109.074 ms 0238: dt=1.792000, rms=0.598 (0.102%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49590.020 ms 0239: dt=1.792000, rms=0.597 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48351.539 ms 0240: dt=3.600000, rms=0.597 (0.136%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44682.684 ms 0241: dt=1.792000, rms=0.596 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44780.980 ms 0242: dt=2.166667, rms=0.596 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52347.770 ms 0243: dt=1.536000, rms=0.596 (0.033%), neg=0, invalid=766 0244: dt=1.536000, rms=0.596 (0.031%), neg=0, invalid=766 0245: dt=1.536000, rms=0.595 (0.035%), neg=0, invalid=766 0246: dt=1.536000, rms=0.595 (0.049%), neg=0, invalid=766 0247: dt=1.536000, rms=0.595 (0.063%), neg=0, invalid=766 0248: dt=1.536000, rms=0.594 (0.058%), neg=0, invalid=766 0249: dt=1.536000, rms=0.594 (0.037%), neg=0, invalid=766 0250: dt=1.536000, rms=0.594 (0.011%), neg=0, invalid=766 0251: dt=1.536000, rms=0.594 (-0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42158.953 ms 0252: dt=0.448000, rms=0.594 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43656.965 ms 0253: dt=0.448000, rms=0.594 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47124.426 ms 0254: dt=0.320000, rms=0.594 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.594, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46812.215 ms 0255: dt=5.120000, rms=0.591 (0.546%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48228.242 ms 0256: dt=1.024000, rms=0.591 (0.015%), neg=0, invalid=766 0257: dt=1.024000, rms=0.591 (0.003%), neg=0, invalid=766 0258: dt=1.024000, rms=0.591 (0.004%), neg=0, invalid=766 0259: dt=1.024000, rms=0.591 (0.007%), neg=0, invalid=766 0260: dt=1.024000, rms=0.590 (0.035%), neg=0, invalid=766 0261: dt=1.024000, rms=0.590 (0.061%), neg=0, invalid=766 0262: dt=1.024000, rms=0.590 (0.082%), neg=0, invalid=766 0263: dt=1.024000, rms=0.589 (0.073%), neg=0, invalid=766 0264: dt=1.024000, rms=0.589 (0.058%), neg=0, invalid=766 0265: dt=1.024000, rms=0.589 (0.024%), neg=0, invalid=766 0266: dt=1.024000, rms=0.589 (-0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45274.695 ms 0267: dt=0.000000, rms=0.589 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.574, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45871.844 ms 0268: dt=0.178504, rms=0.565 (1.592%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43600.086 ms 0269: dt=0.151083, rms=0.560 (0.947%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57935.121 ms 0270: dt=0.134350, rms=0.556 (0.643%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54202.461 ms 0271: dt=0.124504, rms=0.554 (0.487%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47138.570 ms 0272: dt=0.028000, rms=0.553 (0.095%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51940.727 ms 0273: dt=0.116071, rms=0.551 (0.363%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50308.816 ms 0274: dt=0.320000, rms=0.546 (0.856%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54677.914 ms 0275: dt=0.112000, rms=0.545 (0.194%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65028.785 ms 0276: dt=0.320000, rms=0.543 (0.492%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47130.422 ms 0277: dt=0.028000, rms=0.542 (0.033%), neg=0, invalid=766 0278: dt=0.028000, rms=0.542 (0.030%), neg=0, invalid=766 0279: dt=0.028000, rms=0.542 (0.061%), neg=0, invalid=766 0280: dt=0.028000, rms=0.541 (0.084%), neg=0, invalid=766 0281: dt=0.028000, rms=0.541 (0.103%), neg=0, invalid=766 0282: dt=0.028000, rms=0.540 (0.120%), neg=0, invalid=766 0283: dt=0.028000, rms=0.540 (0.127%), neg=0, invalid=766 0284: dt=0.028000, rms=0.539 (0.019%), neg=0, invalid=766 0285: dt=0.028000, rms=0.539 (0.045%), neg=0, invalid=766 0286: dt=0.028000, rms=0.539 (0.063%), neg=0, invalid=766 0287: dt=0.028000, rms=0.538 (0.074%), neg=0, invalid=766 0288: dt=0.028000, rms=0.538 (0.084%), neg=0, invalid=766 0289: dt=0.028000, rms=0.538 (0.092%), neg=0, invalid=766 0290: dt=0.028000, rms=0.537 (0.102%), neg=0, invalid=766 0291: dt=0.028000, rms=0.536 (0.105%), neg=0, invalid=766 0292: dt=0.028000, rms=0.536 (0.110%), neg=0, invalid=766 0293: dt=0.028000, rms=0.535 (0.110%), neg=0, invalid=766 0294: dt=0.028000, rms=0.535 (0.108%), neg=0, invalid=766 0295: dt=0.028000, rms=0.534 (0.111%), neg=0, invalid=766 0296: dt=0.028000, rms=0.533 (0.106%), neg=0, invalid=766 0297: dt=0.028000, rms=0.533 (0.102%), neg=0, invalid=766 0298: dt=0.028000, rms=0.532 (0.096%), neg=0, invalid=766 0299: dt=0.028000, rms=0.532 (0.092%), neg=0, invalid=766 0300: dt=0.028000, rms=0.531 (0.087%), neg=0, invalid=766 0301: dt=0.028000, rms=0.531 (0.083%), neg=0, invalid=766 0302: dt=0.028000, rms=0.531 (0.075%), neg=0, invalid=766 0303: dt=0.028000, rms=0.530 (0.070%), neg=0, invalid=766 0304: dt=0.028000, rms=0.530 (0.066%), neg=0, invalid=766 0305: dt=0.028000, rms=0.530 (0.061%), neg=0, invalid=766 0306: dt=0.028000, rms=0.529 (0.055%), neg=0, invalid=766 0307: dt=0.028000, rms=0.529 (0.053%), neg=0, invalid=766 0308: dt=0.028000, rms=0.529 (0.046%), neg=0, invalid=766 0309: dt=0.028000, rms=0.529 (0.042%), neg=0, invalid=766 0310: dt=0.028000, rms=0.528 (0.041%), neg=0, invalid=766 0311: dt=0.028000, rms=0.528 (0.036%), neg=0, invalid=766 0312: dt=0.028000, rms=0.528 (0.035%), neg=0, invalid=766 0313: dt=0.028000, rms=0.528 (0.030%), neg=0, invalid=766 0314: dt=0.028000, rms=0.528 (0.028%), neg=0, invalid=766 0315: dt=0.028000, rms=0.528 (0.025%), neg=0, invalid=766 0316: dt=0.028000, rms=0.527 (0.023%), neg=0, invalid=766 0317: dt=0.028000, rms=0.527 (0.024%), neg=0, invalid=766 0318: dt=0.028000, rms=0.527 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56546.117 ms 0319: dt=0.448000, rms=0.527 (0.013%), neg=0, invalid=766 0320: dt=0.056000, rms=0.527 (0.003%), neg=0, invalid=766 0321: dt=0.056000, rms=0.527 (0.001%), neg=0, invalid=766 0322: dt=0.056000, rms=0.527 (0.004%), neg=0, invalid=766 0323: dt=0.056000, rms=0.527 (0.005%), neg=0, invalid=766 0324: dt=0.056000, rms=0.527 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.527, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58337.184 ms 0325: dt=0.112000, rms=0.526 (0.266%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60839.574 ms 0326: dt=0.448000, rms=0.522 (0.753%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51924.445 ms 0327: dt=0.000109, rms=0.522 (-0.004%), neg=0, invalid=766 0328: dt=0.000109, rms=0.522 (0.000%), neg=0, invalid=766 0329: dt=0.000109, rms=0.522 (-0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.518, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61236.254 ms iter 0, gcam->neg = 20 after 21 iterations, nbhd size=2, neg = 0 0330: dt=44.800000, rms=0.500 (3.583%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61962.445 ms iter 0, gcam->neg = 39 after 27 iterations, nbhd size=3, neg = 0 0331: dt=44.800000, rms=0.494 (1.117%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 67788.766 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0332: dt=11.200000, rms=0.492 (0.355%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 76724.797 ms 0333: dt=11.200000, rms=0.492 (0.164%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0334: dt=11.200000, rms=0.491 (0.130%), neg=0, invalid=766 0335: dt=11.200000, rms=0.490 (0.224%), neg=0, invalid=766 0336: dt=11.200000, rms=0.489 (0.280%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0337: dt=11.200000, rms=0.487 (0.302%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0338: dt=11.200000, rms=0.486 (0.303%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0339: dt=11.200000, rms=0.484 (0.297%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0340: dt=11.200000, rms=0.483 (0.297%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0341: dt=11.200000, rms=0.482 (0.248%), neg=0, invalid=766 0342: dt=11.200000, rms=0.480 (0.239%), neg=0, invalid=766 0343: dt=11.200000, rms=0.480 (0.184%), neg=0, invalid=766 0344: dt=11.200000, rms=0.479 (0.199%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0345: dt=11.200000, rms=0.478 (0.167%), neg=0, invalid=766 0346: dt=11.200000, rms=0.477 (0.176%), neg=0, invalid=766 0347: dt=11.200000, rms=0.476 (0.143%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0348: dt=11.200000, rms=0.476 (0.141%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0349: dt=11.200000, rms=0.475 (0.103%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0350: dt=11.200000, rms=0.475 (0.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64376.184 ms 0351: dt=11.200000, rms=0.474 (0.055%), neg=0, invalid=766 0352: dt=11.200000, rms=0.474 (0.025%), neg=0, invalid=766 0353: dt=11.200000, rms=0.474 (0.052%), neg=0, invalid=766 0354: dt=11.200000, rms=0.474 (0.049%), neg=0, invalid=766 0355: dt=11.200000, rms=0.474 (0.045%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55642.809 ms iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0356: dt=44.800000, rms=0.470 (0.837%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56778.660 ms 0357: dt=9.600000, rms=0.469 (0.164%), neg=0, invalid=766 0358: dt=9.600000, rms=0.468 (0.082%), neg=0, invalid=766 0359: dt=9.600000, rms=0.468 (0.087%), neg=0, invalid=766 0360: dt=9.600000, rms=0.467 (0.161%), neg=0, invalid=766 0361: dt=9.600000, rms=0.467 (0.099%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0362: dt=9.600000, rms=0.466 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55653.516 ms 0363: dt=9.600000, rms=0.466 (0.074%), neg=0, invalid=766 0364: dt=9.600000, rms=0.466 (0.014%), neg=0, invalid=766 0365: dt=9.600000, rms=0.466 (0.043%), neg=0, invalid=766 0366: dt=9.600000, rms=0.465 (0.060%), neg=0, invalid=766 0367: dt=9.600000, rms=0.465 (0.046%), neg=0, invalid=766 0368: dt=9.600000, rms=0.465 (0.055%), neg=0, invalid=766 0369: dt=9.600000, rms=0.465 (0.034%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59768.230 ms 0370: dt=1.008000, rms=0.474 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63357.078 ms 0371: dt=0.864000, rms=0.475 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62368.297 ms 0372: dt=2.304000, rms=0.474 (0.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69129.594 ms 0373: dt=1.008000, rms=0.474 (0.004%), neg=0, invalid=766 0374: dt=1.008000, rms=0.474 (0.005%), neg=0, invalid=766 0375: dt=1.008000, rms=0.474 (-0.013%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.491, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78976.297 ms 0376: dt=1.024000, rms=0.490 (0.171%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75012.320 ms 0377: dt=0.320000, rms=0.490 (0.012%), neg=0, invalid=766 0378: dt=0.320000, rms=0.490 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80980.891 ms 0379: dt=1.151079, rms=0.489 (0.150%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77649.438 ms 0380: dt=0.320000, rms=0.489 (0.003%), neg=0, invalid=766 0381: dt=0.320000, rms=0.489 (0.005%), neg=0, invalid=766 0382: dt=0.320000, rms=0.489 (-0.017%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75312.898 ms iter 0, gcam->neg = 885 after 12 iterations, nbhd size=1, neg = 0 0383: dt=1.911373, rms=0.431 (8.744%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 82690.664 ms 0384: dt=0.000109, rms=0.431 (0.003%), neg=0, invalid=766 0385: dt=0.000109, rms=0.431 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69169.984 ms 0386: dt=0.000438, rms=0.431 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61667.691 ms 0387: dt=0.000000, rms=0.431 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68997.586 ms iter 0, gcam->neg = 329 after 11 iterations, nbhd size=1, neg = 0 0388: dt=0.492138, rms=0.406 (2.273%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78209.352 ms 0389: dt=0.000750, rms=0.406 (-0.010%), neg=0, invalid=766 0390: dt=0.000750, rms=0.406 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0391: dt=0.000750, rms=0.406 (0.000%), neg=0, invalid=766 0392: dt=0.000750, rms=0.406 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70514.344 ms iter 0, gcam->neg = 61 after 15 iterations, nbhd size=2, neg = 0 0393: dt=0.112000, rms=0.405 (0.249%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 79386.414 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0394: dt=0.001750, rms=0.405 (0.003%), neg=0, invalid=766 0395: dt=0.001750, rms=0.405 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0396: dt=0.001750, rms=0.405 (0.007%), neg=0, invalid=766 0397: dt=0.001750, rms=0.405 (0.011%), neg=0, invalid=766 0398: dt=0.001750, rms=0.405 (0.013%), neg=0, invalid=766 0399: dt=0.001750, rms=0.405 (0.016%), neg=0, invalid=766 0400: dt=0.001750, rms=0.405 (0.016%), neg=0, invalid=766 0401: dt=0.001750, rms=0.405 (0.018%), neg=0, invalid=766 0402: dt=0.001750, rms=0.404 (0.018%), neg=0, invalid=766 0403: dt=0.001750, rms=0.404 (0.021%), neg=0, invalid=766 0404: dt=0.001750, rms=0.404 (0.022%), neg=0, invalid=766 0405: dt=0.001750, rms=0.404 (0.022%), neg=0, invalid=766 0406: dt=0.001750, rms=0.404 (0.022%), neg=0, invalid=766 0407: dt=0.001750, rms=0.404 (0.023%), neg=0, invalid=766 0408: dt=0.001750, rms=0.404 (0.023%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77501.117 ms iter 0, gcam->neg = 90 after 7 iterations, nbhd size=1, neg = 0 0409: dt=0.096000, rms=0.401 (0.457%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71822.312 ms iter 0, gcam->neg = 17 after 6 iterations, nbhd size=1, neg = 0 0410: dt=0.024000, rms=0.401 (0.080%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0411: dt=0.024000, rms=0.401 (0.083%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 6 iterations, nbhd size=1, neg = 0 0412: dt=0.024000, rms=0.400 (0.157%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 7 iterations, nbhd size=1, neg = 0 0413: dt=0.024000, rms=0.399 (0.203%), neg=0, invalid=766 iter 0, gcam->neg = 54 after 14 iterations, nbhd size=2, neg = 0 0414: dt=0.024000, rms=0.398 (0.240%), neg=0, invalid=766 iter 0, gcam->neg = 70 after 8 iterations, nbhd size=1, neg = 0 0415: dt=0.024000, rms=0.397 (0.257%), neg=0, invalid=766 iter 0, gcam->neg = 92 after 8 iterations, nbhd size=1, neg = 0 0416: dt=0.024000, rms=0.396 (0.249%), neg=0, invalid=766 iter 0, gcam->neg = 101 after 9 iterations, nbhd size=1, neg = 0 0417: dt=0.024000, rms=0.395 (0.249%), neg=0, invalid=766 iter 0, gcam->neg = 112 after 8 iterations, nbhd size=1, neg = 0 0418: dt=0.024000, rms=0.394 (0.227%), neg=0, invalid=766 iter 0, gcam->neg = 121 after 9 iterations, nbhd size=1, neg = 0 0419: dt=0.024000, rms=0.394 (0.196%), neg=0, invalid=766 iter 0, gcam->neg = 113 after 28 iterations, nbhd size=3, neg = 0 0420: dt=0.024000, rms=0.393 (0.173%), neg=0, invalid=766 iter 0, gcam->neg = 138 after 20 iterations, nbhd size=2, neg = 0 0421: dt=0.024000, rms=0.392 (0.129%), neg=0, invalid=766 iter 0, gcam->neg = 151 after 16 iterations, nbhd size=2, neg = 0 0422: dt=0.024000, rms=0.392 (0.105%), neg=0, invalid=766 iter 0, gcam->neg = 170 after 33 iterations, nbhd size=3, neg = 0 0423: dt=0.024000, rms=0.392 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62380.609 ms 0424: dt=0.000438, rms=0.392 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64915.828 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=0.000750, rms=0.392 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65209.586 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0426: dt=0.005000, rms=0.392 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72075.555 ms iter 0, gcam->neg = 21 after 14 iterations, nbhd size=2, neg = 0 0427: dt=0.064000, rms=0.391 (0.110%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66352.570 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0428: dt=0.007000, rms=0.391 (0.006%), neg=0, invalid=766 0429: dt=0.007000, rms=0.391 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0430: dt=0.007000, rms=0.391 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0431: dt=0.007000, rms=0.391 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0432: dt=0.007000, rms=0.391 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0433: dt=0.007000, rms=0.391 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 14 iterations, nbhd size=2, neg = 0 0434: dt=0.007000, rms=0.391 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0435: dt=0.007000, rms=0.391 (0.045%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0436: dt=0.007000, rms=0.390 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 8 iterations, nbhd size=1, neg = 0 0437: dt=0.007000, rms=0.390 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 21 iterations, nbhd size=3, neg = 0 0438: dt=0.007000, rms=0.390 (0.026%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66441.812 ms iter 0, gcam->neg = 46 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 37290.031 ms iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.002 (38.565%) gcamFindOptimalTimeStep: Complete in 30371.736 ms iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.001 (19.279%) 0439: dt=9.600000, rms=0.390 (-0.217%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57755.301 ms iter 0, gcam->neg = 53 after 77 iterations, nbhd size=3, neg = 0 0440: dt=19.200000, rms=0.389 (0.295%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60519.234 ms iter 0, gcam->neg = 60 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 37388.223 ms iter 1, dt=0.000031: new neg 1, old_neg 4, delta 3, rms=0.002 (51.689%) gcamFindOptimalTimeStep: Complete in 33018.832 ms iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (53.872%) 0441: dt=19.200000, rms=0.389 (0.093%), neg=0, invalid=766 iter 0, gcam->neg = 22 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 48090.523 ms iter 1, dt=0.000047: new neg 0, old_neg 2, delta 2, rms=0.001 (55.146%) 0442: dt=19.200000, rms=0.388 (0.145%), neg=0, invalid=766 iter 0, gcam->neg = 34 after 200 iterations, nbhd size=1, neg = 15 starting rms=0.008, neg=15, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 37512.117 ms iter 1, dt=0.000047: new neg 0, old_neg 15, delta 15, rms=0.002 (80.320%) 0443: dt=19.200000, rms=0.388 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.006, neg=10, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25923.658 ms iter 1, dt=0.000023: new neg 0, old_neg 10, delta 10, rms=0.002 (69.277%) 0444: dt=19.200000, rms=0.388 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 59 after 200 iterations, nbhd size=3, neg = 17 starting rms=0.009, neg=17, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28095.939 ms iter 1, dt=0.000023: new neg 1, old_neg 17, delta 16, rms=0.002 (76.105%) gcamFindOptimalTimeStep: Complete in 31739.240 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (30.320%) 0445: dt=19.200000, rms=0.388 (-0.071%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50514.250 ms iter 0, gcam->neg = 4 after 35 iterations, nbhd size=4, neg = 0 0446: dt=2.800000, rms=0.388 (-0.003%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54521.629 ms iter 0, gcam->neg = 56 after 200 iterations, nbhd size=1, neg = 12 starting rms=0.008, neg=12, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 32138.883 ms iter 1, dt=0.000039: new neg 0, old_neg 12, delta 12, rms=0.002 (80.480%) 0447: dt=2.000000, rms=0.388 (0.029%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48198.062 ms iter 0, gcam->neg = 52 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.006, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 32492.246 ms iter 1, dt=0.000031: new neg 0, old_neg 3, delta 3, rms=0.001 (76.452%) 0448: dt=1.960000, rms=0.388 (0.126%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51444.672 ms iter 0, gcam->neg = 37 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.007, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 35414.465 ms iter 1, dt=0.000031: new neg 0, old_neg 5, delta 5, rms=0.001 (77.670%) 0449: dt=1.803922, rms=0.387 (0.102%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.007, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31987.369 ms iter 1, dt=0.000031: new neg 0, old_neg 6, delta 6, rms=0.001 (79.122%) 0450: dt=1.803922, rms=0.387 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=3, neg = 9 starting rms=0.006, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 37035.395 ms iter 1, dt=0.000023: new neg 0, old_neg 9, delta 9, rms=0.001 (74.230%) 0451: dt=1.803922, rms=0.387 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 46 iterations, nbhd size=4, neg = 0 0452: dt=1.803922, rms=0.386 (0.086%), neg=0, invalid=766 iter 0, gcam->neg = 73 after 200 iterations, nbhd size=2, neg = 9 starting rms=0.007, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30896.824 ms iter 1, dt=0.000031: new neg 0, old_neg 9, delta 9, rms=0.002 (77.969%) 0453: dt=1.803922, rms=0.386 (-0.026%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57770.500 ms iter 0, gcam->neg = 61 after 200 iterations, nbhd size=1, neg = 8 starting rms=0.008, neg=8, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28566.320 ms iter 1, dt=0.000031: new neg 0, old_neg 8, delta 8, rms=0.001 (82.907%) 0454: dt=3.456000, rms=0.386 (0.197%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52697.383 ms iter 0, gcam->neg = 35 after 200 iterations, nbhd size=2, neg = 8 starting rms=0.007, neg=8, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28135.900 ms iter 1, dt=0.000023: new neg 0, old_neg 8, delta 8, rms=0.001 (83.691%) 0455: dt=2.406780, rms=0.385 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 42 after 200 iterations, nbhd size=4, neg = 8 starting rms=0.007, neg=8, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29093.500 ms iter 1, dt=0.000023: new neg 0, old_neg 8, delta 8, rms=0.001 (84.433%) 0456: dt=2.406780, rms=0.385 (0.091%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 200 iterations, nbhd size=2, neg = 4 starting rms=0.007, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29703.002 ms iter 1, dt=0.000023: new neg 0, old_neg 4, delta 4, rms=0.001 (83.808%) 0457: dt=2.406780, rms=0.384 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 45 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.008, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31129.723 ms iter 1, dt=0.000023: new neg 0, old_neg 9, delta 9, rms=0.001 (84.712%) 0458: dt=2.406780, rms=0.384 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 200 iterations, nbhd size=3, neg = 4 starting rms=0.007, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28629.936 ms iter 1, dt=0.000023: new neg 0, old_neg 4, delta 4, rms=0.001 (85.364%) 0459: dt=2.406780, rms=0.384 (0.071%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.385, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54322.723 ms 0460: dt=0.028000, rms=0.385 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53981.469 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0461: dt=0.112000, rms=0.385 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53872.031 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.006, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29678.957 ms iter 1, dt=0.000023: new neg 0, old_neg 3, delta 3, rms=0.001 (86.886%) 0462: dt=0.112000, rms=0.385 (0.002%), neg=0, invalid=766 0463: dt=0.112000, rms=0.385 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 39405.738 ms iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.001 (87.132%) 0464: dt=0.112000, rms=0.385 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 39230.945 ms iter 1, dt=0.000025: new neg 0, old_neg 1, delta 1, rms=0.001 (56.238%) 0465: dt=0.112000, rms=0.385 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.385, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52821.898 ms iter 0, gcam->neg = 14 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28544.479 ms iter 1, dt=0.000023: new neg 1, old_neg 3, delta 2, rms=0.001 (68.147%) gcamFindOptimalTimeStep: Complete in 29526.820 ms iter 2, dt=0.000492: new neg 0, old_neg 1, delta 1, rms=0.001 (41.436%) 0466: dt=0.397727, rms=0.385 (0.058%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55432.461 ms iter 0, gcam->neg = 22 after 200 iterations, nbhd size=2, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28088.385 ms iter 1, dt=0.000023: new neg 1, old_neg 3, delta 2, rms=0.001 (66.718%) gcamFindOptimalTimeStep: Complete in 26904.568 ms iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.001 (26.602%) 0467: dt=0.448000, rms=0.385 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 40 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 38262.387 ms iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.001 (82.660%) 0468: dt=0.448000, rms=0.385 (-0.064%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53459.086 ms iter 0, gcam->neg = 21 after 7 iterations, nbhd size=1, neg = 0 0469: dt=0.028000, rms=0.382 (0.120%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52528.621 ms iter 0, gcam->neg = 32 after 6 iterations, nbhd size=1, neg = 0 0470: dt=0.048000, rms=0.381 (0.183%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53339.016 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0471: dt=0.004000, rms=0.381 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0472: dt=0.004000, rms=0.381 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0473: dt=0.004000, rms=0.381 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0474: dt=0.004000, rms=0.381 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0475: dt=0.004000, rms=0.381 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0476: dt=0.004000, rms=0.381 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0477: dt=0.004000, rms=0.381 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0478: dt=0.004000, rms=0.380 (0.066%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0479: dt=0.004000, rms=0.380 (0.070%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 13 iterations, nbhd size=2, neg = 0 0480: dt=0.004000, rms=0.380 (0.070%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0481: dt=0.004000, rms=0.379 (0.074%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 8 iterations, nbhd size=1, neg = 0 0482: dt=0.004000, rms=0.379 (0.076%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 7 iterations, nbhd size=1, neg = 0 0483: dt=0.004000, rms=0.379 (0.075%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.379, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53629.305 ms iter 0, gcam->neg = 15 after 15 iterations, nbhd size=2, neg = 0 0484: dt=0.028000, rms=0.379 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58461.113 ms iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0485: dt=0.012000, rms=0.378 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0486: dt=0.012000, rms=0.378 (0.042%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0487: dt=0.012000, rms=0.378 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 7 iterations, nbhd size=1, neg = 0 0488: dt=0.012000, rms=0.378 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 15 iterations, nbhd size=2, neg = 0 0489: dt=0.012000, rms=0.377 (0.113%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 19 iterations, nbhd size=2, neg = 0 0490: dt=0.012000, rms=0.377 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 33 after 17 iterations, nbhd size=2, neg = 0 0491: dt=0.012000, rms=0.376 (0.146%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 6 iterations, nbhd size=1, neg = 0 0492: dt=0.012000, rms=0.375 (0.161%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 7 iterations, nbhd size=1, neg = 0 0493: dt=0.012000, rms=0.375 (0.164%), neg=0, invalid=766 iter 0, gcam->neg = 34 after 9 iterations, nbhd size=1, neg = 0 0494: dt=0.012000, rms=0.374 (0.158%), neg=0, invalid=766 iter 0, gcam->neg = 33 after 17 iterations, nbhd size=2, neg = 0 0495: dt=0.012000, rms=0.374 (0.150%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 9 iterations, nbhd size=1, neg = 0 0496: dt=0.012000, rms=0.373 (0.140%), neg=0, invalid=766 iter 0, gcam->neg = 45 after 21 iterations, nbhd size=3, neg = 0 0497: dt=0.012000, rms=0.373 (0.121%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 23 iterations, nbhd size=3, neg = 0 0498: dt=0.012000, rms=0.372 (0.107%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47787.414 ms 0499: dt=0.001500, rms=0.372 (0.000%), neg=0, invalid=766 0500: dt=0.001500, rms=0.372 (0.000%), neg=0, invalid=766 0501: dt=0.001500, rms=0.372 (0.000%), neg=0, invalid=766 0502: dt=0.001500, rms=0.372 (0.000%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0503: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 0504: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 0505: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 0506: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 0507: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 0508: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 0509: dt=0.001500, rms=0.372 (0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.372, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53394.020 ms iter 0, gcam->neg = 10 after 6 iterations, nbhd size=1, neg = 0 0510: dt=0.016000, rms=0.371 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50485.586 ms iter 0, gcam->neg = 16 after 6 iterations, nbhd size=1, neg = 0 0511: dt=0.028000, rms=0.371 (0.104%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49693.855 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0512: dt=0.007000, rms=0.371 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0513: dt=0.007000, rms=0.371 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0514: dt=0.007000, rms=0.371 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0515: dt=0.007000, rms=0.370 (0.064%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0516: dt=0.007000, rms=0.370 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 14 iterations, nbhd size=2, neg = 0 0517: dt=0.007000, rms=0.370 (0.088%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 15 iterations, nbhd size=2, neg = 0 0518: dt=0.007000, rms=0.369 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 24 iterations, nbhd size=3, neg = 0 0519: dt=0.007000, rms=0.369 (0.097%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 7 iterations, nbhd size=1, neg = 0 0520: dt=0.007000, rms=0.369 (0.106%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 15 iterations, nbhd size=2, neg = 0 0521: dt=0.007000, rms=0.368 (0.106%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 9 iterations, nbhd size=1, neg = 0 0522: dt=0.007000, rms=0.368 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 23 after 8 iterations, nbhd size=1, neg = 0 0523: dt=0.007000, rms=0.367 (0.103%), neg=0, invalid=766 iter 0, gcam->neg = 22 after 17 iterations, nbhd size=2, neg = 0 0524: dt=0.007000, rms=0.367 (0.101%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.367, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49064.609 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0525: dt=0.001750, rms=0.367 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52983.242 ms 0526: dt=0.004000, rms=0.367 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49558.133 ms iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0527: dt=0.006000, rms=0.367 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54477.844 ms iter 0, gcam->neg = 16 after 29 iterations, nbhd size=3, neg = 0 0528: dt=0.019936, rms=0.367 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46899.848 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0529: dt=0.001000, rms=0.367 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0530: dt=0.001000, rms=0.367 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0531: dt=0.001000, rms=0.367 (0.005%), neg=0, invalid=766 0532: dt=0.001000, rms=0.367 (0.007%), neg=0, invalid=766 0533: dt=0.001000, rms=0.367 (0.009%), neg=0, invalid=766 0534: dt=0.001000, rms=0.367 (0.011%), neg=0, invalid=766 0535: dt=0.001000, rms=0.367 (0.013%), neg=0, invalid=766 0536: dt=0.001000, rms=0.367 (0.014%), neg=0, invalid=766 0537: dt=0.001000, rms=0.367 (0.015%), neg=0, invalid=766 0538: dt=0.001000, rms=0.366 (0.016%), neg=0, invalid=766 0539: dt=0.001000, rms=0.366 (0.017%), neg=0, invalid=766 0540: dt=0.001000, rms=0.366 (0.018%), neg=0, invalid=766 0541: dt=0.001000, rms=0.366 (0.018%), neg=0, invalid=766 0542: dt=0.001000, rms=0.366 (0.019%), neg=0, invalid=766 0543: dt=0.001000, rms=0.366 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0544: dt=0.001000, rms=0.366 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0545: dt=0.001000, rms=0.366 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0546: dt=0.001000, rms=0.366 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0547: dt=0.001000, rms=0.366 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0548: dt=0.001000, rms=0.366 (0.020%), neg=0, invalid=766 0549: dt=0.001000, rms=0.366 (0.020%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50900.750 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0550: dt=0.007000, rms=0.365 (0.026%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59540.477 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0551: dt=0.007000, rms=0.365 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0552: dt=0.007000, rms=0.365 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0553: dt=0.007000, rms=0.365 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 7 iterations, nbhd size=1, neg = 0 0554: dt=0.007000, rms=0.365 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 7 iterations, nbhd size=1, neg = 0 0555: dt=0.007000, rms=0.364 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 46 after 8 iterations, nbhd size=1, neg = 0 0556: dt=0.007000, rms=0.364 (0.082%), neg=0, invalid=766 iter 0, gcam->neg = 53 after 8 iterations, nbhd size=1, neg = 0 0557: dt=0.007000, rms=0.364 (0.091%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 16 iterations, nbhd size=2, neg = 0 0558: dt=0.007000, rms=0.363 (0.097%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 16 iterations, nbhd size=2, neg = 0 0559: dt=0.007000, rms=0.363 (0.102%), neg=0, invalid=766 iter 0, gcam->neg = 46 after 19 iterations, nbhd size=2, neg = 0 0560: dt=0.007000, rms=0.363 (0.102%), neg=0, invalid=766 iter 0, gcam->neg = 48 after 29 iterations, nbhd size=3, neg = 0 0561: dt=0.007000, rms=0.362 (0.095%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.362, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54169.516 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0562: dt=0.005000, rms=0.362 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55890.570 ms 0563: dt=0.004000, rms=0.362 (0.014%), neg=0, invalid=766 0564: dt=0.004000, rms=0.362 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 16 iterations, nbhd size=2, neg = 0 0565: dt=0.004000, rms=0.362 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0566: dt=0.004000, rms=0.362 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0567: dt=0.004000, rms=0.362 (0.045%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 23 iterations, nbhd size=3, neg = 0 0568: dt=0.004000, rms=0.362 (0.049%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 13 iterations, nbhd size=2, neg = 0 0569: dt=0.004000, rms=0.361 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 23 iterations, nbhd size=3, neg = 0 0570: dt=0.004000, rms=0.361 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 8 iterations, nbhd size=1, neg = 0 0571: dt=0.004000, rms=0.361 (0.063%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 14 iterations, nbhd size=2, neg = 0 0572: dt=0.004000, rms=0.361 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 48 after 18 iterations, nbhd size=2, neg = 0 0573: dt=0.004000, rms=0.361 (0.056%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 8 hours, 26 minutes and 26 seconds. #-------------------------------------- #@# CA Reg Inv Fri May 20 04:34:24 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri May 20 04:35:40 EDT 2011 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11511184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 21 seconds. #-------------------------------------- #@# SkullLTA Fri May 20 04:37:03 EDT 2011 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (50, 30, 18) --> (206, 200, 226) using (102, 87, 122) as brain centroid... mean wm in atlas = 126, using box (83,66,96) --> (121, 107,147) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10291.2, old_max_log_p =-10350.7 (thresh=-10340.4) 1.144 -0.032 -0.011 -16.131; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10291.2, old_max_log_p =-10291.2 (thresh=-10280.9) 1.144 -0.032 -0.011 -16.131; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10278.4, old_max_log_p =-10291.2 (thresh=-10280.9) 1.081 0.014 -0.005 -13.982; -0.015 1.253 0.093 -28.629; 0.011 -0.090 0.977 -1.074; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10274.8, old_max_log_p =-10278.4 (thresh=-10268.1) 1.100 -0.026 -0.039 -7.848; 0.020 1.232 0.058 -24.718; 0.047 -0.049 0.997 -10.737; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10268.6, old_max_log_p =-10274.8 (thresh=-10264.5) 1.096 -0.026 -0.031 -7.864; 0.020 1.230 0.058 -24.547; 0.038 -0.049 0.998 -9.788; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10268.6 tol 0.000010 Resulting transform: 1.096 -0.026 -0.031 -7.864; 0.020 1.230 0.058 -24.547; 0.038 -0.049 0.998 -9.788; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10268.6 (old=-10350.7) transform before final EM align: 1.096 -0.026 -0.031 -7.864; 0.020 1.230 0.058 -24.547; 0.038 -0.049 0.998 -9.788; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1144172.1 after pass:transform: ( 1.10, -0.02, -0.03, -7.86) ( 0.02, 1.23, 0.06, -24.55) ( 0.04, -0.05, 1.00, -9.79) dfp_em_step_func: 008: -log(p) = 1144170.8 after pass:transform: ( 1.10, -0.02, -0.03, -7.86) ( 0.02, 1.23, 0.06, -24.55) ( 0.04, -0.05, 1.00, -9.79) dfp_em_step_func: 009: -log(p) = 1144169.5 after pass:transform: ( 1.10, -0.02, -0.03, -7.86) ( 0.02, 1.23, 0.06, -24.55) ( 0.04, -0.05, 1.00, -9.79) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 1144169.5 tol 0.000000 final transform: 1.099 -0.023 -0.028 -7.864; 0.019 1.231 0.058 -24.547; 0.038 -0.049 0.999 -9.788; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 24 minutes and 41 seconds. #-------------------------------------- #@# SubCort Seg Fri May 20 05:01:44 EDT 2011 rm -f aseg.mgz aseg.manedit.mgz mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.16024 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (6082 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (6082 voxels, peak = 5), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.16899 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (7260 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (7260 voxels, peak = 5), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.10249 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, peak = 97), gca=97.0 gca peak = 0.18160 (96) mri peak = 0.07222 (100) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (362 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (362 voxels, peak = 98), gca=98.4 gca peak = 0.27536 (62) mri peak = 0.07193 (55) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (1269 voxels, overlap=0.612) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (1269 voxels, peak = 54), gca=54.2 gca peak = 0.32745 (63) mri peak = 0.07922 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1010 voxels, overlap=0.587) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1010 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.09217 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (30723 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (30723 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.07707 (109) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (33170 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (33170 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.03551 (63) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (22153 voxels, overlap=0.857) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (22153 voxels, peak = 60), gca=59.8 gca peak = 0.08598 (64) mri peak = 0.03474 (63) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (23519 voxels, overlap=0.849) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (23519 voxels, peak = 61), gca=60.8 gca peak = 0.24164 (71) mri peak = 0.10499 (72) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1160 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1160 voxels, peak = 69), gca=69.2 gca peak = 0.18227 (75) mri peak = 0.07028 (65) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1320 voxels, overlap=0.433) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1320 voxels, peak = 64), gca=63.8 gca peak = 0.10629 (62) mri peak = 0.05144 (57) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (19176 voxels, overlap=0.971) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (19176 voxels, peak = 59), gca=58.9 gca peak = 0.11668 (59) mri peak = 0.05258 (56) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21544 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21544 voxels, peak = 56), gca=56.0 gca peak = 0.17849 (88) mri peak = 0.12410 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4350 voxels, overlap=0.720) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4350 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.11798 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4395 voxels, overlap=0.723) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4395 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.11416 (56) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (484 voxels, overlap=0.583) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (484 voxels, peak = 59), gca=59.2 gca peak = 0.42394 (62) mri peak = 0.09966 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (593 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (593 voxels, peak = 56), gca=55.8 gca peak = 0.10041 (96) mri peak = 0.06293 (90) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3800 voxels, overlap=0.813) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3800 voxels, peak = 91), gca=91.2 gca peak = 0.13978 (88) mri peak = 0.05972 (88) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3582 voxels, overlap=0.984) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3582 voxels, peak = 86), gca=85.8 gca peak = 0.08514 (81) mri peak = 0.05452 (72) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2114 voxels, overlap=0.455) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2114 voxels, peak = 73), gca=72.9 gca peak = 0.09624 (82) mri peak = 0.06283 (71) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2180 voxels, overlap=0.606) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2180 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.06087 (85) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9734 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9734 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.08869 (101) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1074 voxels, overlap=0.698) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1074 voxels, peak = 100), gca=99.7 gca peak = 0.17004 (92) mri peak = 0.10259 (100) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1061 voxels, overlap=0.857) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1061 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.13542 ( 6) Third_Ventricle (14): linear fit = 0.32 x + 0.0 (191 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.32 x + 0.0 (191 voxels, peak = 12), gca=11.7 gca peak = 0.26069 (23) mri peak = 0.22599 ( 8) Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (469 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (469 voxels, peak = 7), gca=6.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.92 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.16024 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6082 voxels, overlap=0.777) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6082 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.16899 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.65 x + 0.0 (7260 voxels, overlap=0.825) Right_Lateral_Ventricle (43): linear fit = 0.65 x + 0.0 (7260 voxels, peak = 6), gca=5.8 gca peak = 0.26236 (97) mri peak = 0.10249 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, peak = 97), gca=97.0 gca peak = 0.16124 (98) mri peak = 0.07222 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (362 voxels, overlap=0.993) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (362 voxels, peak = 98), gca=98.0 gca peak = 0.30443 (54) mri peak = 0.07193 (55) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1269 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1269 voxels, peak = 54), gca=54.0 gca peak = 0.30366 (58) mri peak = 0.07922 (61) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1010 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1010 voxels, peak = 55), gca=55.1 gca peak = 0.08347 (108) mri peak = 0.09217 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (30723 voxels, overlap=0.777) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (30723 voxels, peak = 108), gca=108.0 gca peak = 0.08790 (111) mri peak = 0.07707 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33170 voxels, overlap=0.753) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33170 voxels, peak = 111), gca=111.0 gca peak = 0.08255 (60) mri peak = 0.03551 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22153 voxels, overlap=0.971) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22153 voxels, peak = 62), gca=61.5 gca peak = 0.09370 (61) mri peak = 0.03474 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23519 voxels, overlap=0.924) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23519 voxels, peak = 63), gca=62.5 gca peak = 0.26772 (69) mri peak = 0.10499 (72) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1160 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1160 voxels, peak = 67), gca=67.3 gca peak = 0.17680 (64) mri peak = 0.07028 (65) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1320 voxels, overlap=0.995) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1320 voxels, peak = 64), gca=64.0 gca peak = 0.11076 (58) mri peak = 0.05144 (57) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19176 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19176 voxels, peak = 59), gca=59.4 gca peak = 0.12352 (57) mri peak = 0.05258 (56) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (21544 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (21544 voxels, peak = 58), gca=58.4 gca peak = 0.16852 (92) mri peak = 0.12410 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4350 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4350 voxels, peak = 92), gca=92.0 gca peak = 0.15715 (93) mri peak = 0.11798 (93) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4395 voxels, overlap=0.995) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4395 voxels, peak = 91), gca=90.7 gca peak = 0.41356 (59) mri peak = 0.11416 (56) Left_Amygdala (18): linear fit = 0.95 x + 0.0 (484 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 0.95 x + 0.0 (484 voxels, peak = 56), gca=56.0 gca peak = 0.53825 (56) mri peak = 0.09966 (57) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (593 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (593 voxels, peak = 56), gca=56.0 gca peak = 0.10151 (91) mri peak = 0.06293 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3800 voxels, overlap=0.994) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3800 voxels, peak = 91), gca=91.0 gca peak = 0.11274 (83) mri peak = 0.05972 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3582 voxels, overlap=0.998) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3582 voxels, peak = 83), gca=83.0 gca peak = 0.09324 (74) mri peak = 0.05452 (72) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2114 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2114 voxels, peak = 74), gca=74.0 gca peak = 0.11772 (70) mri peak = 0.06283 (71) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2180 voxels, overlap=0.989) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2180 voxels, peak = 70), gca=70.0 gca peak = 0.07366 (90) mri peak = 0.06087 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9734 voxels, overlap=0.855) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9734 voxels, peak = 90), gca=90.0 gca peak = 0.10381 (99) mri peak = 0.08869 (101) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1074 voxels, overlap=0.799) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1074 voxels, peak = 101), gca=101.5 gca peak = 0.13263 (99) mri peak = 0.10259 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1061 voxels, overlap=0.881) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1061 voxels, peak = 99), gca=99.0 gca peak = 0.35640 (14) mri peak = 0.13542 ( 6) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (191 voxels, overlap=0.658) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (191 voxels, peak = 11), gca=10.8 gca peak = 0.33827 ( 9) mri peak = 0.22599 ( 8) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (469 voxels, overlap=0.756) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (469 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24950 (33) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.53035 (60) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.62747 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.33086 (28) gca peak Right_Accumbens_area = 0.32731 (70) gca peak Right_vessel = 0.77757 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.13994 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.66 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 14107 gm and wm labels changed (%17 to gray, %83 to white out of all changed labels) 364 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 83308 changed. image ll: -2.207, PF=1.000 pass 2: 14017 changed. image ll: -2.206, PF=1.000 pass 3: 5523 changed. pass 4: 2404 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 23 minutes and 7 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/cc_up.lta good_output will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/cc_up.lta reading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/norm.mgz 6218 voxels in left wm, 15857 in right wm, xrange [125, 130] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 global minimum found at slice 127.0, rotations (-0.29, 0.45) final transformation (x=127.0, yr=-0.294, zr=0.453): 1.000 -0.008 -0.005 2.322; 0.008 1.000 -0.000 30.003; 0.005 -0.000 1.000 20.349; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 145 176 eigenvectors: 0.000 -0.010 1.000; -0.004 -1.000 -0.010; 1.000 -0.004 -0.001; writing aseg with callosum to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Fri May 20 05:25:37 EDT 2011 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri May 20 05:25:37 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 2421 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 3 minutes and 42 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 109 gm peak at 61 (61), valley at 35 (35) csf peak at 10, setting threshold to 44 white matter peak found at 111 white matter peak found at 110 gm peak at 61 (61), valley at 36 (36) csf peak at 10, setting threshold to 44 #-------------------------------------------- #@# Mask BFS Fri May 20 05:29:25 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1526273 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri May 20 05:29:28 EDT 2011 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.1 +- 5.2 [80.0 --> 125.0] GM (70.0) : 68.0 +- 10.4 [30.0 --> 96.0] setting bottom of white matter range to 78.4 setting top of gray matter range to 88.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 3893 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6100 filled 3965 bright non-wm voxels segmented. 2442 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz auto filling took 0.70 minutes reading wm segmentation from wm.seg.mgz... 237 voxels added to wm to prevent paths from MTL structures to cortex 2149 additional wm voxels added 0 additional wm voxels added SEG EDIT: 88029 voxels turned on, 28858 voxels turned off. writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 47 found - 47 modified | TOTAL: 47 pass 2 (xy+): 0 found - 47 modified | TOTAL: 47 pass 1 (xy-): 34 found - 34 modified | TOTAL: 81 pass 2 (xy-): 0 found - 34 modified | TOTAL: 81 pass 1 (yz+): 60 found - 60 modified | TOTAL: 141 pass 2 (yz+): 0 found - 60 modified | TOTAL: 141 pass 1 (yz-): 34 found - 34 modified | TOTAL: 175 pass 2 (yz-): 0 found - 34 modified | TOTAL: 175 pass 1 (xz+): 26 found - 26 modified | TOTAL: 201 pass 2 (xz+): 0 found - 26 modified | TOTAL: 201 pass 1 (xz-): 25 found - 25 modified | TOTAL: 226 pass 2 (xz-): 0 found - 25 modified | TOTAL: 226 Iteration Number : 1 pass 1 (+++): 27 found - 27 modified | TOTAL: 27 pass 2 (+++): 0 found - 27 modified | TOTAL: 27 pass 1 (+++): 11 found - 11 modified | TOTAL: 38 pass 2 (+++): 0 found - 11 modified | TOTAL: 38 pass 1 (+++): 25 found - 25 modified | TOTAL: 63 pass 2 (+++): 0 found - 25 modified | TOTAL: 63 pass 1 (+++): 15 found - 15 modified | TOTAL: 78 pass 2 (+++): 0 found - 15 modified | TOTAL: 78 Iteration Number : 1 pass 1 (++): 97 found - 97 modified | TOTAL: 97 pass 2 (++): 0 found - 97 modified | TOTAL: 97 pass 1 (+-): 102 found - 102 modified | TOTAL: 199 pass 2 (+-): 2 found - 104 modified | TOTAL: 201 pass 3 (+-): 0 found - 104 modified | TOTAL: 201 pass 1 (--): 93 found - 93 modified | TOTAL: 294 pass 2 (--): 0 found - 93 modified | TOTAL: 294 pass 1 (-+): 88 found - 88 modified | TOTAL: 382 pass 2 (-+): 0 found - 88 modified | TOTAL: 382 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 9 found - 9 modified | TOTAL: 12 pass 2 (xy-): 0 found - 9 modified | TOTAL: 12 pass 1 (yz+): 6 found - 6 modified | TOTAL: 18 pass 2 (yz+): 0 found - 6 modified | TOTAL: 18 pass 1 (yz-): 7 found - 7 modified | TOTAL: 25 pass 2 (yz-): 0 found - 7 modified | TOTAL: 25 pass 1 (xz+): 4 found - 4 modified | TOTAL: 29 pass 2 (xz+): 0 found - 4 modified | TOTAL: 29 pass 1 (xz-): 3 found - 3 modified | TOTAL: 32 pass 2 (xz-): 0 found - 3 modified | TOTAL: 32 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 4 found - 4 modified | TOTAL: 7 pass 2 (+-): 0 found - 4 modified | TOTAL: 7 pass 1 (--): 3 found - 3 modified | TOTAL: 10 pass 2 (--): 0 found - 3 modified | TOTAL: 10 pass 1 (-+): 2 found - 2 modified | TOTAL: 12 pass 2 (-+): 0 found - 2 modified | TOTAL: 12 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 738 (out of 517434: 0.142627) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri May 20 05:32:00 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1587 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) need search nearby using seed (125, 107, 89), TAL = (3.0, -39.0, 21.0) talairach voxel to voxel transform 0.939 0.023 0.008 6.599; -0.019 0.792 -0.074 25.113; -0.010 0.072 0.998 3.164; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 107, 89) --> (3.0, -39.0, 21.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (3.00, -39.00, 21.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -39.00, 21.00) SRC: (110.26, 101.34, 98.64) search lh wm seed point around talairach space (-15.00, -39.00, 21.00), SRC: (144.07, 100.66, 98.28) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri May 20 05:33:03 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 5 found - 5 modified | TOTAL: 9 pass 2 (xz+): 0 found - 5 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 12 (out of 247623: 0.004846) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 40: 1034 vertices, 1132 faces slice 50: 5493 vertices, 5714 faces slice 60: 12035 vertices, 12247 faces slice 70: 20133 vertices, 20498 faces slice 80: 29126 vertices, 29445 faces slice 90: 37981 vertices, 38268 faces slice 100: 47432 vertices, 47819 faces slice 110: 59125 vertices, 59487 faces slice 120: 70104 vertices, 70509 faces slice 130: 80471 vertices, 80824 faces slice 140: 90425 vertices, 90816 faces slice 150: 99214 vertices, 99515 faces slice 160: 106400 vertices, 106685 faces slice 170: 113260 vertices, 113508 faces slice 180: 119192 vertices, 119388 faces slice 190: 123332 vertices, 123487 faces slice 200: 125180 vertices, 125221 faces slice 210: 125198 vertices, 125230 faces slice 220: 125198 vertices, 125230 faces slice 230: 125198 vertices, 125230 faces slice 240: 125198 vertices, 125230 faces slice 250: 125198 vertices, 125230 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 125198 voxel in cpt #1: X=-32 [v=125198,e=375690,f=250460] located at (-27.158892, -15.059450, 24.124859) For the whole surface: X=-32 [v=125198,e=375690,f=250460] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri May 20 05:33:14 EDT 2011 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri May 20 05:33:19 EDT 2011 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts avg radius = 46.0 mm, total surface area = 66215 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri May 20 05:34:19 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.58 (0.00-->7.04) (max @ vno 39400 --> 40270) face area 0.03 +- 0.03 (-0.05-->0.71) scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.337, avgs=0 005/300: dt: 0.9000, rms radial error=177.076, avgs=0 010/300: dt: 0.9000, rms radial error=176.517, avgs=0 015/300: dt: 0.9000, rms radial error=175.783, avgs=0 020/300: dt: 0.9000, rms radial error=174.948, avgs=0 025/300: dt: 0.9000, rms radial error=174.056, avgs=0 030/300: dt: 0.9000, rms radial error=173.132, avgs=0 035/300: dt: 0.9000, rms radial error=172.191, avgs=0 040/300: dt: 0.9000, rms radial error=171.241, avgs=0 045/300: dt: 0.9000, rms radial error=170.290, avgs=0 050/300: dt: 0.9000, rms radial error=169.340, avgs=0 055/300: dt: 0.9000, rms radial error=168.392, avgs=0 060/300: dt: 0.9000, rms radial error=167.448, avgs=0 065/300: dt: 0.9000, rms radial error=166.508, avgs=0 070/300: dt: 0.9000, rms radial error=165.572, avgs=0 075/300: dt: 0.9000, rms radial error=164.641, avgs=0 080/300: dt: 0.9000, rms radial error=163.715, avgs=0 085/300: dt: 0.9000, rms radial error=162.794, avgs=0 090/300: dt: 0.9000, rms radial error=161.878, avgs=0 095/300: dt: 0.9000, rms radial error=160.967, avgs=0 100/300: dt: 0.9000, rms radial error=160.061, avgs=0 105/300: dt: 0.9000, rms radial error=159.160, avgs=0 110/300: dt: 0.9000, rms radial error=158.263, avgs=0 115/300: dt: 0.9000, rms radial error=157.372, avgs=0 120/300: dt: 0.9000, rms radial error=156.485, avgs=0 125/300: dt: 0.9000, rms radial error=155.604, avgs=0 130/300: dt: 0.9000, rms radial error=154.726, avgs=0 135/300: dt: 0.9000, rms radial error=153.854, avgs=0 140/300: dt: 0.9000, rms radial error=152.988, avgs=0 145/300: dt: 0.9000, rms radial error=152.127, avgs=0 150/300: dt: 0.9000, rms radial error=151.270, avgs=0 155/300: dt: 0.9000, rms radial error=150.420, avgs=0 160/300: dt: 0.9000, rms radial error=149.574, avgs=0 165/300: dt: 0.9000, rms radial error=148.734, avgs=0 170/300: dt: 0.9000, rms radial error=147.897, avgs=0 175/300: dt: 0.9000, rms radial error=147.066, avgs=0 180/300: dt: 0.9000, rms radial error=146.239, avgs=0 185/300: dt: 0.9000, rms radial error=145.416, avgs=0 190/300: dt: 0.9000, rms radial error=144.598, avgs=0 195/300: dt: 0.9000, rms radial error=143.784, avgs=0 200/300: dt: 0.9000, rms radial error=142.974, avgs=0 205/300: dt: 0.9000, rms radial error=142.170, avgs=0 210/300: dt: 0.9000, rms radial error=141.369, avgs=0 215/300: dt: 0.9000, rms radial error=140.573, avgs=0 220/300: dt: 0.9000, rms radial error=139.781, avgs=0 225/300: dt: 0.9000, rms radial error=138.994, avgs=0 230/300: dt: 0.9000, rms radial error=138.211, avgs=0 235/300: dt: 0.9000, rms radial error=137.432, avgs=0 240/300: dt: 0.9000, rms radial error=136.658, avgs=0 245/300: dt: 0.9000, rms radial error=135.888, avgs=0 250/300: dt: 0.9000, rms radial error=135.123, avgs=0 255/300: dt: 0.9000, rms radial error=134.361, avgs=0 260/300: dt: 0.9000, rms radial error=133.604, avgs=0 265/300: dt: 0.9000, rms radial error=132.851, avgs=0 270/300: dt: 0.9000, rms radial error=132.102, avgs=0 275/300: dt: 0.9000, rms radial error=131.357, avgs=0 280/300: dt: 0.9000, rms radial error=130.617, avgs=0 285/300: dt: 0.9000, rms radial error=129.881, avgs=0 290/300: dt: 0.9000, rms radial error=129.148, avgs=0 295/300: dt: 0.9000, rms radial error=128.420, avgs=0 300/300: dt: 0.9000, rms radial error=127.696, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14541.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2386.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 236.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00883 epoch 4 (K=640.0), pass 1, starting sse = 13.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/15 = 0.00953 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri May 20 05:40:36 EDT 2011 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 good_output lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-32 (nv=125198, nf=250460, ne=375690, g=17) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 2901 ambiguous faces found in tessellation segmenting defects... 31 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 12 -merging segment 15 into 14 29 defects to be corrected 0 vertices coincident reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4694 (-4.7347) -vertex loglikelihood: -6.5843 (-3.2921) -normal dot loglikelihood: -3.6006 (-3.6006) -quad curv loglikelihood: -6.3897 (-3.1949) Total Loglikelihood : -26.0440 CORRECTING DEFECT 0 (vertices=36, convex hull=63) After retessellation of defect 0, euler #=-26 (123415,369508,246067) : difference with theory (-26) = 0 CORRECTING DEFECT 1 (vertices=38, convex hull=85) After retessellation of defect 1, euler #=-25 (123427,369578,246126) : difference with theory (-25) = 0 CORRECTING DEFECT 2 (vertices=263, convex hull=186) After retessellation of defect 2, euler #=-24 (123502,369886,246360) : difference with theory (-24) = 0 CORRECTING DEFECT 3 (vertices=36, convex hull=70) After retessellation of defect 3, euler #=-23 (123524,369979,246432) : difference with theory (-23) = 0 CORRECTING DEFECT 4 (vertices=67, convex hull=87) After retessellation of defect 4, euler #=-22 (123564,370136,246550) : difference with theory (-22) = 0 CORRECTING DEFECT 5 (vertices=20, convex hull=64) After retessellation of defect 5, euler #=-21 (123573,370189,246595) : difference with theory (-21) = 0 CORRECTING DEFECT 6 (vertices=127, convex hull=155) After retessellation of defect 6, euler #=-20 (123621,370410,246769) : difference with theory (-20) = 0 CORRECTING DEFECT 7 (vertices=57, convex hull=76) After retessellation of defect 7, euler #=-19 (123645,370512,246848) : difference with theory (-19) = 0 CORRECTING DEFECT 8 (vertices=45, convex hull=35) After retessellation of defect 8, euler #=-18 (123650,370540,246872) : difference with theory (-18) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=26) After retessellation of defect 9, euler #=-17 (123651,370550,246882) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=6, convex hull=14) After retessellation of defect 10, euler #=-16 (123654,370561,246891) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=78) After retessellation of defect 11, euler #=-15 (123675,370657,246967) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=100, convex hull=159) After retessellation of defect 12, euler #=-13 (123712,370845,247120) : difference with theory (-14) = -1 CORRECTING DEFECT 13 (vertices=477, convex hull=162) normal vector of length zero at vertex 124336 with 3 faces After retessellation of defect 13, euler #=-12 (123721,370960,247227) : difference with theory (-13) = -1 CORRECTING DEFECT 14 (vertices=19, convex hull=24) Warning - incorrect dp selected!!!!(-73.826619 >= -73.826621 ) After retessellation of defect 14, euler #=-11 (123724,370976,247241) : difference with theory (-12) = -1 CORRECTING DEFECT 15 (vertices=37, convex hull=60) After retessellation of defect 15, euler #=-10 (123733,371027,247284) : difference with theory (-11) = -1 CORRECTING DEFECT 16 (vertices=39, convex hull=86) After retessellation of defect 16, euler #=-9 (123742,371091,247340) : difference with theory (-10) = -1 CORRECTING DEFECT 17 (vertices=8, convex hull=13) After retessellation of defect 17, euler #=-8 (123745,371102,247349) : difference with theory (-9) = -1 CORRECTING DEFECT 18 (vertices=9, convex hull=20) After retessellation of defect 18, euler #=-7 (123746,371111,247358) : difference with theory (-8) = -1 CORRECTING DEFECT 19 (vertices=45, convex hull=61) After retessellation of defect 19, euler #=-6 (123763,371184,247415) : difference with theory (-7) = -1 CORRECTING DEFECT 20 (vertices=161, convex hull=49) After retessellation of defect 20, euler #=-6 (123779,371257,247472) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=53, convex hull=33) After retessellation of defect 21, euler #=-5 (123789,371305,247511) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=6, convex hull=18) After retessellation of defect 22, euler #=-4 (123790,371314,247520) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=21, convex hull=59) After retessellation of defect 23, euler #=-3 (123799,371364,247562) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=24, convex hull=28) After retessellation of defect 24, euler #=-2 (123801,371380,247577) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=18, convex hull=17) After retessellation of defect 25, euler #=-1 (123803,371389,247585) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=25, convex hull=25) After retessellation of defect 26, euler #=0 (123808,371409,247601) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=6, convex hull=16) After retessellation of defect 27, euler #=1 (123809,371416,247608) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=19, convex hull=19) After retessellation of defect 28, euler #=2 (123810,371424,247616) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.02-->16.57) (max @ vno 88168 --> 94578) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.02-->16.57) (max @ vno 88168 --> 94578) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 109 mutations (33.9%), 213 crossovers (66.1%), 188 vertices were eliminated building final representation... 1388 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=123810, nf=247616, ne=371424, g=0) writing corrected surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.1 minutes 0 defective edges removing intersecting faces 000: 161 intersecting 001: 6 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 123810 - 371424 + 247616 = 2 --> 0 holes F =2V-4: 247616 = 247620-4 (0) 2E=3F: 742848 = 742848 (0) total defect index = 0 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 16 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri May 20 06:06:52 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs good_output lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11431 bright wm thresholded. 4601 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig... computing class statistics... border white: 235426 voxels (1.40%) border gray 265557 voxels (1.58%) WM (91.0): 92.7 +- 8.9 [70.0 --> 110.0] GM (78.0) : 75.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.5 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 23.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.23) (max @ vno 33803 --> 123603) face area 0.28 +- 0.12 (0.00-->2.34) mean absolute distance = 0.87 +- 1.06 3182 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=62 using class modes intead of means.... mean inside = 91.3, mean outside = 71.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=73.4, 184 (184) missing vertices, mean dist 0.4 [0.8 (%26.7)->0.9 (%73.3))] %53 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.03-->4.40) (max @ vno 96736 --> 96733) face area 0.28 +- 0.14 (0.00-->3.22) mean absolute distance = 0.40 +- 0.72 2577 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6130499.5, rms=12.91 001: dt: 0.5000, sse=6116969.5, rms=9.67 002: dt: 0.5000, sse=6160021.0, rms=7.50 003: dt: 0.5000, sse=6341568.0, rms=5.99 004: dt: 0.5000, sse=6467678.5, rms=5.01 005: dt: 0.5000, sse=6681245.0, rms=4.42 006: dt: 0.5000, sse=6780402.0, rms=4.09 007: dt: 0.5000, sse=6914337.5, rms=3.90 008: dt: 0.5000, sse=6924771.0, rms=3.80 009: dt: 0.5000, sse=6980174.5, rms=3.72 rms = 3.68, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6926578.5, rms=3.68 011: dt: 0.2500, sse=4308608.5, rms=2.53 012: dt: 0.2500, sse=3921864.2, rms=2.21 013: dt: 0.2500, sse=3734878.0, rms=2.13 rms = 2.08, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3668373.0, rms=2.08 015: dt: 0.1250, sse=3585097.0, rms=2.01 rms = 2.01, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3547295.5, rms=2.01 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=77.0, 209 (106) missing vertices, mean dist -0.2 [0.5 (%71.2)->0.3 (%28.8))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.07-->4.82) (max @ vno 96736 --> 96735) face area 0.36 +- 0.17 (0.00-->5.49) mean absolute distance = 0.31 +- 0.45 2554 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4229183.5, rms=5.30 017: dt: 0.5000, sse=4597746.5, rms=3.38 rms = 3.55, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4219007.5, rms=2.62 019: dt: 0.2500, sse=4023212.5, rms=2.06 020: dt: 0.2500, sse=3919617.5, rms=1.79 021: dt: 0.2500, sse=3859391.5, rms=1.71 rms = 1.67, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3836451.8, rms=1.67 023: dt: 0.1250, sse=3774332.5, rms=1.61 rms = 1.61, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3748644.8, rms=1.61 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 206 (97) missing vertices, mean dist -0.2 [0.3 (%74.3)->0.2 (%25.7))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.10-->5.54) (max @ vno 96736 --> 96735) face area 0.35 +- 0.17 (0.00-->6.10) mean absolute distance = 0.23 +- 0.34 2512 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4144291.2, rms=4.51 025: dt: 0.5000, sse=4368648.5, rms=3.10 rms = 3.43, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4042799.8, rms=2.12 027: dt: 0.2500, sse=3945392.2, rms=1.66 028: dt: 0.2500, sse=3910350.2, rms=1.47 rms = 1.48, time step reduction 2 of 3 to 0.125... rms = 1.44, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=3878991.2, rms=1.44 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.9, 195 (90) missing vertices, mean dist -0.1 [0.3 (%58.6)->0.2 (%41.4))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3923324.0, rms=2.12 rms = 2.38, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3967959.5, rms=1.46 031: dt: 0.2500, sse=4141836.5, rms=1.08 rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4136438.2, rms=1.07 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 20 non-cortical segments detected only using segment with 1727 vertices erasing segment 1 (vno[0] = 44500) erasing segment 2 (vno[0] = 60369) erasing segment 3 (vno[0] = 63858) erasing segment 4 (vno[0] = 76575) erasing segment 5 (vno[0] = 77376) erasing segment 6 (vno[0] = 83213) erasing segment 7 (vno[0] = 84061) erasing segment 8 (vno[0] = 86038) erasing segment 9 (vno[0] = 86123) erasing segment 10 (vno[0] = 87151) erasing segment 11 (vno[0] = 89173) erasing segment 12 (vno[0] = 91171) erasing segment 13 (vno[0] = 91996) erasing segment 14 (vno[0] = 94472) erasing segment 15 (vno[0] = 95243) erasing segment 16 (vno[0] = 96737) erasing segment 17 (vno[0] = 97491) erasing segment 18 (vno[0] = 98209) erasing segment 19 (vno[0] = 98827) writing cortex label to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.cortex.label... LabelWrite: saving to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.cortex.label writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.area vertex spacing 0.91 +- 0.26 (0.06-->5.68) (max @ vno 96736 --> 96735) face area 0.34 +- 0.17 (0.00-->6.14) refinement took 6.1 minutes #-------------------------------------------- #@# Smooth2 lh Fri May 20 06:12:57 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Fri May 20 06:13:02 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.1 mm, total surface area = 77265 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.9 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 275 vertices thresholded to be in k1 ~ [-0.21 0.39], k2 ~ [-0.13 0.06] total integrated curvature = 0.579*4pi (7.273) --> 0 handles ICI = 1.4, FI = 8.1, variation=142.214 145 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 126 vertices thresholded to be in [-0.15 0.18] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Fri May 20 06:15:29 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm good_output lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ good_output/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.020046 WARN: S explicit min: 0.000000 vertex = 263 #-------------------------------------------- #@# Sphere lh Fri May 20 06:15:37 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.15 hours scaling brain by 0.292... pass 1: epoch 1 of 3 starting distance error %19.27 pass 1: epoch 2 of 3 starting distance error %19.18 unfolding complete - removing small folds... starting distance error %19.17 removing remaining folds... final distance error %19.18 #-------------------------------------------- #@# Surf Reg lh Fri May 20 07:24:50 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_register -curv ../surf/lh.sphere /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.597 curvature mean = 0.031, std = 0.937 curvature mean = 0.019, std = 0.874 curvature mean = 0.026, std = 0.970 curvature mean = 0.008, std = 0.946 curvature mean = 0.025, std = 0.983 curvature mean = 0.003, std = 0.976 curvature mean = 0.025, std = 0.987 curvature mean = 0.001, std = 0.989 curvature mean = -0.026, std = 0.290 curvature mean = 0.004, std = 0.068 curvature mean = 0.062, std = 0.348 curvature mean = 0.004, std = 0.080 curvature mean = 0.028, std = 0.541 curvature mean = 0.004, std = 0.086 curvature mean = 0.015, std = 0.677 curvature mean = 0.004, std = 0.088 curvature mean = 0.005, std = 0.781 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri May 20 08:11:22 EDT 2011 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri May 20 08:11:26 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mrisp_paint -a 5 /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri May 20 08:11:30 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1150 labels changed using aseg relabeling using gibbs priors... 000: 2735 changed, 123810 examined... 001: 617 changed, 11889 examined... 002: 129 changed, 3469 examined... 003: 40 changed, 802 examined... 004: 18 changed, 245 examined... 005: 3 changed, 117 examined... 006: 1 changed, 18 examined... 007: 0 changed, 7 examined... 245 labels changed using aseg 000: 109 total segments, 67 labels (253 vertices) changed 001: 41 total segments, 3 labels (12 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1818 vertices marked for relabeling... 1818 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 56 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri May 20 08:12:27 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs good_output lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11431 bright wm thresholded. 4601 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig... computing class statistics... border white: 235426 voxels (1.40%) border gray 265557 voxels (1.58%) WM (91.0): 92.7 +- 8.9 [70.0 --> 110.0] GM (78.0) : 75.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.3 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.5 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 23.8 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=62 using class modes intead of means.... mean inside = 91.3, mean outside = 71.1 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.23) (max @ vno 33803 --> 123603) face area 0.28 +- 0.12 (0.00-->2.34) mean absolute distance = 0.87 +- 1.07 3273 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 439 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown mean border=73.4, 184 (184) missing vertices, mean dist 0.4 [0.9 (%26.7)->0.9 (%73.3))] %54 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.03-->4.40) (max @ vno 96736 --> 96733) face area 0.28 +- 0.14 (0.00-->3.22) mean absolute distance = 0.40 +- 0.72 2599 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6146148.0, rms=12.90 001: dt: 0.5000, sse=6133057.0, rms=9.66 002: dt: 0.5000, sse=6174317.5, rms=7.49 003: dt: 0.5000, sse=6358561.0, rms=5.99 004: dt: 0.5000, sse=6483288.5, rms=5.00 005: dt: 0.5000, sse=6700163.0, rms=4.41 006: dt: 0.5000, sse=6804722.5, rms=4.09 007: dt: 0.5000, sse=6937177.5, rms=3.90 008: dt: 0.5000, sse=6949818.0, rms=3.80 009: dt: 0.5000, sse=7006079.0, rms=3.72 rms = 3.67, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6952690.0, rms=3.67 011: dt: 0.2500, sse=4322867.5, rms=2.53 012: dt: 0.2500, sse=3935279.8, rms=2.21 013: dt: 0.2500, sse=3748289.2, rms=2.13 rms = 2.08, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3681845.0, rms=2.08 015: dt: 0.1250, sse=3598792.5, rms=2.01 rms = 2.01, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3560954.0, rms=2.01 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 5 with 27 points - only 0.00% unknown deleting segment 6 with 197 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 41 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 12 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=77.0, 208 (106) missing vertices, mean dist -0.2 [0.5 (%71.1)->0.3 (%28.9))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.07-->5.21) (max @ vno 96736 --> 96733) face area 0.36 +- 0.17 (0.00-->4.52) mean absolute distance = 0.31 +- 0.45 2574 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4247104.0, rms=5.29 017: dt: 0.5000, sse=4617809.0, rms=3.37 rms = 3.55, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4237211.0, rms=2.62 019: dt: 0.2500, sse=4041327.0, rms=2.06 020: dt: 0.2500, sse=3938580.8, rms=1.79 021: dt: 0.2500, sse=3880684.2, rms=1.71 rms = 1.67, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3854188.0, rms=1.67 023: dt: 0.1250, sse=3792112.0, rms=1.62 rms = 1.61, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3767814.5, rms=1.61 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 283 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 49 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 21 points - only 0.00% unknown deleting segment 8 with 53 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown mean border=80.6, 207 (97) missing vertices, mean dist -0.2 [0.3 (%74.3)->0.2 (%25.7))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.10-->5.45) (max @ vno 96736 --> 96733) face area 0.35 +- 0.17 (0.00-->4.79) mean absolute distance = 0.23 +- 0.34 2541 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4166982.5, rms=4.51 025: dt: 0.5000, sse=4393000.0, rms=3.09 rms = 3.43, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4067378.2, rms=2.12 027: dt: 0.2500, sse=3970182.5, rms=1.67 028: dt: 0.2500, sse=3935924.2, rms=1.48 rms = 1.48, time step reduction 2 of 3 to 0.125... rms = 1.44, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=3904537.8, rms=1.44 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 320 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 76 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 61 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown mean border=81.9, 197 (90) missing vertices, mean dist -0.1 [0.3 (%58.6)->0.2 (%41.4))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3948939.8, rms=2.12 rms = 2.38, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3993798.8, rms=1.46 031: dt: 0.2500, sse=4172823.0, rms=1.09 rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4166888.2, rms=1.07 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=51.9, 197 (197) missing vertices, mean dist 1.9 [0.2 (%0.0)->2.1 (%100.0))] %22 local maxima, %61 large gradients and %12 min vals, 896 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=23082524.0, rms=29.61 001: dt: 0.5000, sse=17121214.0, rms=24.95 002: dt: 0.5000, sse=12786170.0, rms=20.96 003: dt: 0.5000, sse=9861929.0, rms=17.67 004: dt: 0.5000, sse=8200891.5, rms=14.99 005: dt: 0.5000, sse=7249660.0, rms=12.78 006: dt: 0.5000, sse=6601484.5, rms=10.96 007: dt: 0.5000, sse=6202385.0, rms=9.42 008: dt: 0.5000, sse=5945184.0, rms=8.03 009: dt: 0.5000, sse=5788488.5, rms=6.87 010: dt: 0.5000, sse=5770776.0, rms=5.94 011: dt: 0.5000, sse=5797260.0, rms=5.27 012: dt: 0.5000, sse=5863478.0, rms=4.78 013: dt: 0.5000, sse=5941807.0, rms=4.48 014: dt: 0.5000, sse=6018239.5, rms=4.26 015: dt: 0.5000, sse=6065876.0, rms=4.12 016: dt: 0.5000, sse=6080176.0, rms=4.01 017: dt: 0.5000, sse=6092707.5, rms=3.95 018: dt: 0.5000, sse=6101862.5, rms=3.88 rms = 3.85, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6102387.0, rms=3.85 020: dt: 0.2500, sse=4093443.2, rms=3.00 021: dt: 0.2500, sse=3874134.8, rms=2.80 rms = 2.76, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3750000.2, rms=2.76 023: dt: 0.1250, sse=3611559.0, rms=2.64 rms = 2.63, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3584740.5, rms=2.63 positioning took 2.5 minutes mean border=48.8, 392 (28) missing vertices, mean dist 0.2 [0.2 (%44.9)->0.6 (%55.1))] %47 local maxima, %40 large gradients and % 7 min vals, 362 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4372505.5, rms=5.66 025: dt: 0.5000, sse=4515512.0, rms=4.22 026: dt: 0.5000, sse=5649883.5, rms=4.00 rms = 4.07, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4638477.5, rms=3.24 028: dt: 0.2500, sse=4270010.5, rms=2.93 029: dt: 0.2500, sse=4206290.0, rms=2.84 rms = 2.81, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4182317.0, rms=2.81 031: dt: 0.1250, sse=4058302.2, rms=2.69 rms = 2.66, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4047898.0, rms=2.66 positioning took 0.9 minutes mean border=46.1, 528 (24) missing vertices, mean dist 0.2 [0.2 (%37.3)->0.4 (%62.7))] %65 local maxima, %22 large gradients and % 7 min vals, 377 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4353195.5, rms=4.34 033: dt: 0.5000, sse=4490687.5, rms=3.87 rms = 3.89, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4220972.5, rms=3.05 035: dt: 0.2500, sse=4319981.5, rms=2.73 036: dt: 0.2500, sse=4307639.0, rms=2.65 rms = 2.63, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4330492.5, rms=2.63 038: dt: 0.1250, sse=4217772.0, rms=2.51 rms = 2.48, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4203208.5, rms=2.48 positioning took 0.8 minutes mean border=44.7, 1097 (20) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.3 (%55.9))] %72 local maxima, %15 large gradients and % 7 min vals, 332 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4272761.0, rms=3.01 rms = 3.57, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4152937.0, rms=2.64 041: dt: 0.2500, sse=4226258.0, rms=2.49 rms = 2.44, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4296352.5, rms=2.44 043: dt: 0.1250, sse=4230339.0, rms=2.35 rms = 2.32, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4225594.5, rms=2.32 positioning took 0.6 minutes writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.area.pial vertex spacing 1.02 +- 0.42 (0.08-->7.37) (max @ vno 83166 --> 82272) face area 0.41 +- 0.30 (0.00-->9.56) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 123810 vertices processed 25000 of 123810 vertices processed 50000 of 123810 vertices processed 75000 of 123810 vertices processed 100000 of 123810 vertices processed 0 of 123810 vertices processed 25000 of 123810 vertices processed 50000 of 123810 vertices processed 75000 of 123810 vertices processed 100000 of 123810 vertices processed thickness calculation complete, 512:531 truncations. 53442 vertices at 0 distance 81063 vertices at 1 distance 65027 vertices at 2 distance 23506 vertices at 3 distance 7225 vertices at 4 distance 2436 vertices at 5 distance 964 vertices at 6 distance 451 vertices at 7 distance 239 vertices at 8 distance 172 vertices at 9 distance 146 vertices at 10 distance 100 vertices at 11 distance 54 vertices at 12 distance 48 vertices at 13 distance 31 vertices at 14 distance 23 vertices at 15 distance 22 vertices at 16 distance 17 vertices at 17 distance 12 vertices at 18 distance 9 vertices at 19 distance 19 vertices at 20 distance writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.thickness positioning took 11.5 minutes #-------------------------------------------- #@# Surf Volume lh Fri May 20 08:23:55 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Fri May 20 08:23:56 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab good_output lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1669 1171 2741 2.352 0.448 0.111 0.029 14 1.9 bankssts 939 608 1477 2.418 0.598 0.145 0.060 29 2.9 caudalanteriorcingulate 2944 1982 5306 2.446 0.550 0.137 0.051 39 5.8 caudalmiddlefrontal 1732 1158 2101 1.619 0.402 0.155 0.055 27 4.0 cuneus 605 411 1976 3.356 0.856 0.143 0.047 8 1.2 entorhinal 4381 3060 8553 2.444 0.702 0.146 0.056 73 9.1 fusiform 6163 4295 11073 2.333 0.516 0.147 0.066 115 18.1 inferiorparietal 4817 3353 10583 2.730 0.731 0.170 0.079 119 14.8 inferiortemporal 1347 901 2385 2.426 0.875 0.155 0.059 23 3.0 isthmuscingulate 5652 3850 8620 2.011 0.521 0.153 0.057 93 11.9 lateraloccipital 2984 2130 5936 2.424 0.599 0.167 0.076 91 9.6 lateralorbitofrontal 3768 2684 5319 1.835 0.559 0.155 0.062 112 9.7 lingual 3316 2237 6293 2.433 0.994 0.165 0.118 157 16.3 medialorbitofrontal 4340 3077 9743 2.684 0.640 0.160 0.067 86 10.5 middletemporal 1139 755 1748 1.925 0.656 0.098 0.026 9 1.4 parahippocampal 1934 1241 3139 2.272 0.561 0.131 0.064 44 6.3 paracentral 2153 1478 3864 2.316 0.448 0.140 0.054 35 4.6 parsopercularis 855 571 1713 2.372 0.542 0.152 0.058 19 2.1 parsorbitalis 1681 1174 2999 2.234 0.484 0.145 0.050 25 3.5 parstriangularis 1348 916 1241 1.449 0.364 0.138 0.048 18 2.7 pericalcarine 6247 4148 9087 1.981 0.582 0.135 0.045 75 12.2 postcentral 1548 1098 2982 2.415 0.743 0.173 0.067 37 4.4 posteriorcingulate 6546 4299 11709 2.491 0.484 0.122 0.043 67 11.6 precentral 5308 3717 9667 2.382 0.595 0.157 0.061 89 13.5 precuneus 1192 814 2540 2.669 0.565 0.170 0.081 55 4.0 rostralanteriorcingulate 6907 4807 12797 2.260 0.564 0.163 0.104 259 19.2 rostralmiddlefrontal 8741 6185 18338 2.547 0.633 0.148 0.064 154 21.2 superiorfrontal 7599 5206 12670 2.190 0.559 0.144 0.052 110 15.5 superiorparietal 6257 4182 11544 2.394 0.632 0.133 0.047 94 13.0 superiortemporal 6305 4313 12011 2.456 0.535 0.159 0.072 129 21.0 supramarginal 266 192 735 2.612 0.495 0.183 0.098 7 0.7 frontalpole 703 496 2472 3.440 0.686 0.148 0.061 10 1.5 temporalpole 631 386 1136 2.495 0.444 0.145 0.052 11 1.3 transversetemporal 3458 2259 6195 2.595 0.814 0.120 0.053 45 5.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri May 20 08:24:14 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 32 labels changed using aseg relabeling using gibbs priors... 000: 8728 changed, 123810 examined... 001: 2173 changed, 33533 examined... 002: 615 changed, 11000 examined... 003: 257 changed, 3489 examined... 004: 148 changed, 1444 examined... 005: 88 changed, 838 examined... 006: 49 changed, 482 examined... 007: 26 changed, 277 examined... 008: 15 changed, 136 examined... 009: 8 changed, 84 examined... 010: 6 changed, 48 examined... 011: 4 changed, 36 examined... 012: 0 changed, 17 examined... 11 labels changed using aseg 000: 272 total segments, 187 labels (1987 vertices) changed 001: 97 total segments, 12 labels (65 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 103 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1139 vertices marked for relabeling... 1139 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 3 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri May 20 08:25:17 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab good_output lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1239 831 2188 2.222 0.640 0.163 0.256 145 3.4 G_and_S_frontomargin 1499 1014 2456 2.111 0.578 0.142 0.055 21 2.7 G_and_S_occipital_inf 1484 967 2541 2.177 0.547 0.138 0.052 19 3.2 G_and_S_paracentral 1419 949 2908 2.591 0.542 0.156 0.061 25 3.7 G_and_S_subcentral 641 462 1400 2.337 0.590 0.197 0.086 17 2.3 G_and_S_transv_frontopol 2354 1601 4171 2.378 0.542 0.138 0.052 31 4.9 G_and_S_cingul-Ant 1105 765 1941 2.323 0.586 0.134 0.050 19 2.1 G_and_S_cingul-Mid-Ant 1162 822 2141 2.405 0.600 0.146 0.053 17 2.5 G_and_S_cingul-Mid-Post 479 337 1309 2.993 0.645 0.198 0.085 13 1.5 G_cingul-Post-dorsal 316 195 420 2.089 0.878 0.155 0.077 6 0.9 G_cingul-Post-ventral 1518 1039 2063 1.669 0.379 0.169 0.064 29 4.1 G_cuneus 1222 814 2576 2.464 0.446 0.150 0.056 22 2.5 G_front_inf-Opercular 353 230 849 2.757 0.442 0.200 0.091 15 1.3 G_front_inf-Orbital 1024 733 2151 2.346 0.451 0.169 0.081 26 3.5 G_front_inf-Triangul 3446 2416 7701 2.492 0.572 0.175 0.084 86 11.0 G_front_middle 6285 4430 14769 2.711 0.598 0.162 0.082 155 20.4 G_front_sup 527 340 1048 2.550 0.623 0.122 0.047 7 0.9 G_Ins_lg_and_S_cent_ins 594 374 1722 3.286 0.822 0.165 0.079 20 1.4 G_insular_short 1634 1132 3506 2.474 0.468 0.168 0.081 47 4.2 G_occipital_middle 1552 1051 2303 1.969 0.484 0.166 0.054 26 3.4 G_occipital_sup 1834 1231 3988 2.550 0.685 0.150 0.062 37 4.2 G_oc-temp_lat-fusifor 2565 1773 3739 1.819 0.598 0.163 0.072 96 7.7 G_oc-temp_med-Lingual 1195 789 2925 2.714 1.026 0.122 0.062 15 2.1 G_oc-temp_med-Parahip 2187 1532 4985 2.480 0.614 0.183 0.092 87 8.9 G_orbital 1947 1359 4291 2.490 0.543 0.178 0.106 54 10.3 G_pariet_inf-Angular 3601 2468 7590 2.510 0.530 0.168 0.082 88 13.5 G_pariet_inf-Supramar 2734 1889 5684 2.482 0.487 0.159 0.065 54 6.7 G_parietal_sup 2255 1460 3486 1.968 0.472 0.139 0.050 30 4.8 G_postcentral 2308 1463 5114 2.724 0.429 0.138 0.063 32 5.7 G_precentral 2702 1929 6142 2.561 0.555 0.185 0.080 63 9.4 G_precuneus 1104 795 2634 2.471 0.733 0.182 0.129 36 3.9 G_rectus 348 228 672 2.861 1.001 0.277 0.409 107 7.7 G_subcallosal 501 290 950 2.485 0.423 0.143 0.057 10 1.2 G_temp_sup-G_T_transv 2499 1671 5171 2.431 0.666 0.143 0.054 43 6.0 G_temp_sup-Lateral 715 480 1618 2.867 0.815 0.124 0.057 11 1.5 G_temp_sup-Plan_polar 979 699 1898 2.405 0.467 0.141 0.056 17 3.0 G_temp_sup-Plan_tempo 2909 2048 7308 2.854 0.762 0.191 0.105 97 11.7 G_temporal_inf 2781 1999 7067 2.837 0.603 0.181 0.080 72 8.2 G_temporal_middle 372 249 524 2.088 0.442 0.109 0.020 2 0.3 Lat_Fis-ant-Horizont 319 224 418 1.947 0.406 0.118 0.027 2 0.4 Lat_Fis-ant-Vertical 1403 939 1767 2.232 0.495 0.124 0.039 12 2.2 Lat_Fis-post 1847 1257 2427 1.713 0.462 0.159 0.062 30 4.3 Pole_occipital 1787 1259 5428 3.208 0.705 0.163 0.068 32 4.6 Pole_temporal 1473 1026 1696 1.740 0.696 0.134 0.044 16 2.6 S_calcarine 3104 2082 3586 1.934 0.598 0.109 0.030 20 4.0 S_central 1049 731 1488 2.066 0.537 0.112 0.027 7 1.3 S_cingul-Marginalis 594 391 1047 2.727 0.651 0.111 0.033 3 0.8 S_circular_insula_ant 1645 1075 2110 2.139 0.666 0.099 0.032 13 2.6 S_circular_insula_inf 1578 1045 2114 2.341 0.452 0.114 0.034 11 2.2 S_circular_insula_sup 805 567 1607 2.653 0.728 0.137 0.054 13 1.4 S_collat_transv_ant 365 261 400 1.772 0.361 0.135 0.038 3 0.6 S_collat_transv_post 1877 1288 2901 2.200 0.470 0.140 0.047 25 3.6 S_front_inf 970 691 1663 2.124 0.586 0.143 0.049 12 1.9 S_front_middle 2502 1737 3942 2.237 0.581 0.119 0.034 21 3.5 S_front_sup 309 216 472 2.428 0.479 0.172 0.098 5 1.6 S_interm_prim-Jensen 2269 1545 3101 2.119 0.580 0.127 0.041 24 3.7 S_intrapariet_and_P_trans 655 447 918 2.133 0.486 0.149 0.044 8 1.2 S_oc_middle_and_Lunatus 1220 819 1521 1.971 0.481 0.111 0.031 8 1.6 S_oc_sup_and_transversal 462 323 695 2.140 0.390 0.127 0.037 5 0.6 S_occipital_ant 796 560 1330 2.384 0.545 0.149 0.049 10 1.5 S_oc-temp_lat 2341 1703 3072 1.932 0.528 0.126 0.038 27 3.5 S_oc-temp_med_and_Lingual 407 276 580 2.104 0.358 0.121 0.034 3 0.6 S_orbital_lateral 1032 689 1685 2.332 1.231 0.126 0.077 31 3.2 S_orbital_med-olfact 878 642 1543 2.293 0.574 0.165 0.066 15 2.2 S_orbital-H_Shaped 1826 1243 2356 2.047 0.669 0.141 0.046 21 3.4 S_parieto_occipital 1287 814 1588 2.353 0.881 0.158 0.069 43 4.2 S_pericallosal 3293 2191 4581 2.119 0.512 0.134 0.041 35 5.8 S_postcentral 1620 1105 2473 2.302 0.409 0.111 0.030 12 2.0 S_precentral-inf-part 824 594 1128 2.213 0.345 0.103 0.020 4 0.8 S_precentral-sup-part 551 367 820 2.147 0.747 0.158 0.054 9 1.4 S_suborbital 1150 794 1748 2.189 0.464 0.131 0.038 11 1.8 S_subparietal 1251 863 1917 2.334 0.521 0.126 0.035 13 1.7 S_temporal_inf 6283 4332 10128 2.312 0.510 0.124 0.038 72 9.8 S_temporal_sup 314 202 493 2.623 0.556 0.142 0.046 4 0.6 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Fri May 20 08:25:37 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 3 found - 3 modified | TOTAL: 3 pass 2 (-+): 0 found - 3 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 255244: 0.002742) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 40: 633 vertices, 692 faces slice 50: 4513 vertices, 4720 faces slice 60: 10859 vertices, 11076 faces slice 70: 18395 vertices, 18715 faces slice 80: 27325 vertices, 27617 faces slice 90: 35992 vertices, 36304 faces slice 100: 45341 vertices, 45710 faces slice 110: 56449 vertices, 56812 faces slice 120: 67220 vertices, 67624 faces slice 130: 77691 vertices, 78051 faces slice 140: 87532 vertices, 87917 faces slice 150: 97334 vertices, 97665 faces slice 160: 104926 vertices, 105217 faces slice 170: 112392 vertices, 112654 faces slice 180: 118908 vertices, 119105 faces slice 190: 124081 vertices, 124267 faces slice 200: 127053 vertices, 127110 faces slice 210: 127172 vertices, 127200 faces slice 220: 127172 vertices, 127200 faces slice 230: 127172 vertices, 127200 faces slice 240: 127172 vertices, 127200 faces slice 250: 127172 vertices, 127200 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 127172 voxel in cpt #1: X=-28 [v=127172,e=381600,f=254400] located at (27.551363, -11.773260, 24.548721) For the whole surface: X=-28 [v=127172,e=381600,f=254400] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri May 20 08:25:48 EDT 2011 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Fri May 20 08:25:53 EDT 2011 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts avg radius = 46.7 mm, total surface area = 67569 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri May 20 08:26:47 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.57 (0.00-->5.87) (max @ vno 41076 --> 42048) face area 0.03 +- 0.03 (-0.05-->0.49) scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.049, avgs=0 005/300: dt: 0.9000, rms radial error=176.788, avgs=0 010/300: dt: 0.9000, rms radial error=176.229, avgs=0 015/300: dt: 0.9000, rms radial error=175.495, avgs=0 020/300: dt: 0.9000, rms radial error=174.658, avgs=0 025/300: dt: 0.9000, rms radial error=173.764, avgs=0 030/300: dt: 0.9000, rms radial error=172.841, avgs=0 035/300: dt: 0.9000, rms radial error=171.904, avgs=0 040/300: dt: 0.9000, rms radial error=170.959, avgs=0 045/300: dt: 0.9000, rms radial error=170.012, avgs=0 050/300: dt: 0.9000, rms radial error=169.065, avgs=0 055/300: dt: 0.9000, rms radial error=168.121, avgs=0 060/300: dt: 0.9000, rms radial error=167.181, avgs=0 065/300: dt: 0.9000, rms radial error=166.244, avgs=0 070/300: dt: 0.9000, rms radial error=165.313, avgs=0 075/300: dt: 0.9000, rms radial error=164.386, avgs=0 080/300: dt: 0.9000, rms radial error=163.464, avgs=0 085/300: dt: 0.9000, rms radial error=162.547, avgs=0 090/300: dt: 0.9000, rms radial error=161.635, avgs=0 095/300: dt: 0.9000, rms radial error=160.728, avgs=0 100/300: dt: 0.9000, rms radial error=159.826, avgs=0 105/300: dt: 0.9000, rms radial error=158.929, avgs=0 110/300: dt: 0.9000, rms radial error=158.037, avgs=0 115/300: dt: 0.9000, rms radial error=157.150, avgs=0 120/300: dt: 0.9000, rms radial error=156.268, avgs=0 125/300: dt: 0.9000, rms radial error=155.390, avgs=0 130/300: dt: 0.9000, rms radial error=154.517, avgs=0 135/300: dt: 0.9000, rms radial error=153.649, avgs=0 140/300: dt: 0.9000, rms radial error=152.786, avgs=0 145/300: dt: 0.9000, rms radial error=151.927, avgs=0 150/300: dt: 0.9000, rms radial error=151.073, avgs=0 155/300: dt: 0.9000, rms radial error=150.224, avgs=0 160/300: dt: 0.9000, rms radial error=149.379, avgs=0 165/300: dt: 0.9000, rms radial error=148.539, avgs=0 170/300: dt: 0.9000, rms radial error=147.704, avgs=0 175/300: dt: 0.9000, rms radial error=146.873, avgs=0 180/300: dt: 0.9000, rms radial error=146.047, avgs=0 185/300: dt: 0.9000, rms radial error=145.225, avgs=0 190/300: dt: 0.9000, rms radial error=144.408, avgs=0 195/300: dt: 0.9000, rms radial error=143.596, avgs=0 200/300: dt: 0.9000, rms radial error=142.788, avgs=0 205/300: dt: 0.9000, rms radial error=141.984, avgs=0 210/300: dt: 0.9000, rms radial error=141.185, avgs=0 215/300: dt: 0.9000, rms radial error=140.390, avgs=0 220/300: dt: 0.9000, rms radial error=139.599, avgs=0 225/300: dt: 0.9000, rms radial error=138.813, avgs=0 230/300: dt: 0.9000, rms radial error=138.031, avgs=0 235/300: dt: 0.9000, rms radial error=137.254, avgs=0 240/300: dt: 0.9000, rms radial error=136.481, avgs=0 245/300: dt: 0.9000, rms radial error=135.712, avgs=0 250/300: dt: 0.9000, rms radial error=134.948, avgs=0 255/300: dt: 0.9000, rms radial error=134.187, avgs=0 260/300: dt: 0.9000, rms radial error=133.431, avgs=0 265/300: dt: 0.9000, rms radial error=132.679, avgs=0 270/300: dt: 0.9000, rms radial error=131.932, avgs=0 275/300: dt: 0.9000, rms radial error=131.188, avgs=0 280/300: dt: 0.9000, rms radial error=130.449, avgs=0 285/300: dt: 0.9000, rms radial error=129.714, avgs=0 290/300: dt: 0.9000, rms radial error=128.983, avgs=0 295/300: dt: 0.9000, rms radial error=128.256, avgs=0 300/300: dt: 0.9000, rms radial error=127.533, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14766.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 2 (K=40.0), pass 1, starting sse = 2410.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 240.93 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/14 = 0.01051 epoch 4 (K=640.0), pass 1, starting sse = 12.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/12 = 0.00982 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri May 20 08:32:30 EDT 2011 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 good_output rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-28 (nv=127172, nf=254400, ne=381600, g=15) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 2513 ambiguous faces found in tessellation segmenting defects... 34 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 33 defects to be corrected 0 vertices coincident reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4371 (-4.7186) -vertex loglikelihood: -6.4819 (-3.2410) -normal dot loglikelihood: -3.6269 (-3.6269) -quad curv loglikelihood: -6.4496 (-3.2248) Total Loglikelihood : -25.9956 CORRECTING DEFECT 0 (vertices=31, convex hull=58) After retessellation of defect 0, euler #=-31 (125614,376260,250615) : difference with theory (-30) = 1 CORRECTING DEFECT 1 (vertices=30, convex hull=56) After retessellation of defect 1, euler #=-30 (125626,376315,250659) : difference with theory (-29) = 1 CORRECTING DEFECT 2 (vertices=42, convex hull=32) After retessellation of defect 2, euler #=-29 (125631,376339,250679) : difference with theory (-28) = 1 CORRECTING DEFECT 3 (vertices=28, convex hull=61) After retessellation of defect 3, euler #=-28 (125641,376394,250725) : difference with theory (-27) = 1 CORRECTING DEFECT 4 (vertices=6, convex hull=18) After retessellation of defect 4, euler #=-27 (125641,376396,250728) : difference with theory (-26) = 1 CORRECTING DEFECT 5 (vertices=45, convex hull=70) After retessellation of defect 5, euler #=-26 (125666,376500,250808) : difference with theory (-25) = 1 CORRECTING DEFECT 6 (vertices=18, convex hull=45) After retessellation of defect 6, euler #=-25 (125677,376552,250850) : difference with theory (-24) = 1 CORRECTING DEFECT 7 (vertices=46, convex hull=78) After retessellation of defect 7, euler #=-24 (125709,376686,250953) : difference with theory (-23) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=23) After retessellation of defect 8, euler #=-23 (125710,376694,250961) : difference with theory (-22) = 1 CORRECTING DEFECT 9 (vertices=7, convex hull=16) After retessellation of defect 9, euler #=-22 (125712,376703,250969) : difference with theory (-21) = 1 CORRECTING DEFECT 10 (vertices=60, convex hull=50) After retessellation of defect 10, euler #=-20 (125720,376755,251015) : difference with theory (-20) = 0 CORRECTING DEFECT 11 (vertices=66, convex hull=35) After retessellation of defect 11, euler #=-19 (125731,376806,251056) : difference with theory (-19) = 0 CORRECTING DEFECT 12 (vertices=23, convex hull=21) After retessellation of defect 12, euler #=-18 (125735,376822,251069) : difference with theory (-18) = 0 CORRECTING DEFECT 13 (vertices=77, convex hull=87) After retessellation of defect 13, euler #=-17 (125773,376975,251185) : difference with theory (-17) = 0 CORRECTING DEFECT 14 (vertices=6, convex hull=26) After retessellation of defect 14, euler #=-16 (125774,376985,251195) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=59, convex hull=33) After retessellation of defect 15, euler #=-15 (125783,377030,251232) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=506, convex hull=111) After retessellation of defect 16, euler #=-14 (125795,377119,251310) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=40, convex hull=17) After retessellation of defect 17, euler #=-13 (125798,377132,251321) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=9, convex hull=17) After retessellation of defect 18, euler #=-12 (125800,377141,251329) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=11, convex hull=18) After retessellation of defect 19, euler #=-11 (125803,377155,251341) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=38, convex hull=71) After retessellation of defect 20, euler #=-10 (125819,377233,251404) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=29, convex hull=70) After retessellation of defect 21, euler #=-9 (125834,377308,251465) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=67, convex hull=43) After retessellation of defect 22, euler #=-8 (125843,377352,251501) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=80, convex hull=70) After retessellation of defect 23, euler #=-7 (125875,377478,251596) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=9, convex hull=12) After retessellation of defect 24, euler #=-6 (125875,377480,251599) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=15, convex hull=16) After retessellation of defect 25, euler #=-5 (125876,377486,251605) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=24, convex hull=69) After retessellation of defect 26, euler #=-4 (125890,377555,251661) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=86, convex hull=87) After retessellation of defect 27, euler #=-3 (125910,377651,251738) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=19, convex hull=53) After retessellation of defect 28, euler #=-2 (125918,377694,251774) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=18, convex hull=29) After retessellation of defect 29, euler #=-1 (125922,377717,251794) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=20, convex hull=35) After retessellation of defect 30, euler #=0 (125925,377737,251812) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=5, convex hull=18) After retessellation of defect 31, euler #=1 (125925,377742,251818) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=39, convex hull=62) After retessellation of defect 32, euler #=2 (125936,377802,251868) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.06-->7.30) (max @ vno 103589 --> 105650) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.06-->7.30) (max @ vno 103589 --> 105650) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 99 mutations (35.2%), 182 crossovers (64.8%), 81 vertices were eliminated building final representation... 1236 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125936, nf=251868, ne=377802, g=0) writing corrected surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 18.8 minutes 0 defective edges removing intersecting faces 000: 149 intersecting 001: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 125936 - 377802 + 251868 = 2 --> 0 holes F =2V-4: 251868 = 251872-4 (0) 2E=3F: 755604 = 755604 (0) total defect index = 0 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 16 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri May 20 08:51:29 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs good_output rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11215 bright wm thresholded. 4651 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig... computing class statistics... border white: 235426 voxels (1.40%) border gray 265557 voxels (1.58%) WM (92.0): 92.8 +- 9.0 [70.0 --> 110.0] GM (77.0) : 75.3 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.4 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 37.8 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->2.94) (max @ vno 104941 --> 105650) face area 0.28 +- 0.12 (0.00-->1.39) mean absolute distance = 0.85 +- 1.06 3098 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=63 using class modes intead of means.... mean inside = 91.5, mean outside = 71.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=74.1, 77 (77) missing vertices, mean dist 0.4 [0.9 (%26.3)->0.8 (%73.7))] %49 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.10-->3.74) (max @ vno 94138 --> 95060) face area 0.28 +- 0.14 (0.00-->1.92) mean absolute distance = 0.40 +- 0.75 2925 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5801948.5, rms=12.36 001: dt: 0.5000, sse=5839185.0, rms=9.15 002: dt: 0.5000, sse=6022707.0, rms=7.10 003: dt: 0.5000, sse=6282106.0, rms=5.70 004: dt: 0.5000, sse=6392652.0, rms=4.80 005: dt: 0.5000, sse=6589760.0, rms=4.24 006: dt: 0.5000, sse=6678592.0, rms=3.96 007: dt: 0.5000, sse=6789412.5, rms=3.77 008: dt: 0.5000, sse=6794292.0, rms=3.70 009: dt: 0.5000, sse=6835774.5, rms=3.62 rms = 3.59, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6824046.0, rms=3.59 011: dt: 0.2500, sse=4138952.0, rms=2.39 012: dt: 0.2500, sse=3737445.5, rms=2.05 013: dt: 0.2500, sse=3559217.0, rms=1.96 014: dt: 0.2500, sse=3498164.0, rms=1.90 rms = 1.88, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3461460.2, rms=1.88 016: dt: 0.1250, sse=3389258.0, rms=1.82 rms = 1.81, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3371618.2, rms=1.81 positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.6, 35 (9) missing vertices, mean dist -0.3 [0.5 (%71.2)->0.3 (%28.8))] %61 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.08-->4.31) (max @ vno 51216 --> 52434) face area 0.36 +- 0.17 (0.00-->2.49) mean absolute distance = 0.31 +- 0.46 2884 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4061283.5, rms=5.20 018: dt: 0.5000, sse=4346773.0, rms=3.24 rms = 3.40, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3994198.0, rms=2.52 020: dt: 0.2500, sse=3818926.0, rms=1.95 021: dt: 0.2500, sse=3697446.8, rms=1.69 022: dt: 0.2500, sse=3651490.8, rms=1.60 rms = 1.56, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3616770.5, rms=1.56 024: dt: 0.1250, sse=3571397.8, rms=1.51 rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3550548.0, rms=1.50 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.1, 41 (3) missing vertices, mean dist -0.2 [0.3 (%73.8)->0.2 (%26.2))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.06-->4.56) (max @ vno 51216 --> 52434) face area 0.35 +- 0.16 (0.00-->2.48) mean absolute distance = 0.24 +- 0.34 2675 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3938818.0, rms=4.40 026: dt: 0.5000, sse=4161201.2, rms=2.97 rms = 3.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3856557.0, rms=2.03 028: dt: 0.2500, sse=3743758.2, rms=1.57 029: dt: 0.2500, sse=3714023.8, rms=1.39 rms = 1.38, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3696223.5, rms=1.38 031: dt: 0.1250, sse=3654366.8, rms=1.32 rms = 1.33, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3654366.8, rms=1.32 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.4, 51 (2) missing vertices, mean dist -0.1 [0.3 (%59.5)->0.2 (%40.5))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3705157.5, rms=2.12 rms = 2.23, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3767663.0, rms=1.44 034: dt: 0.2500, sse=3917509.0, rms=1.01 rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3915270.5, rms=1.00 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 1763 vertices erasing segment 1 (vno[0] = 61344) erasing segment 2 (vno[0] = 76991) erasing segment 3 (vno[0] = 79761) erasing segment 4 (vno[0] = 88642) erasing segment 5 (vno[0] = 88815) erasing segment 6 (vno[0] = 89604) erasing segment 7 (vno[0] = 90571) erasing segment 8 (vno[0] = 92337) erasing segment 9 (vno[0] = 93214) erasing segment 10 (vno[0] = 99686) erasing segment 11 (vno[0] = 125748) erasing segment 12 (vno[0] = 125767) writing cortex label to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.cortex.label... LabelWrite: saving to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.cortex.label writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.area vertex spacing 0.90 +- 0.26 (0.06-->4.59) (max @ vno 51216 --> 52434) face area 0.34 +- 0.16 (0.00-->2.44) refinement took 6.4 minutes #-------------------------------------------- #@# Smooth2 rh Fri May 20 08:57:52 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Fri May 20 08:57:58 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.9 mm, total surface area = 78370 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.9 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 277 vertices thresholded to be in k1 ~ [-0.23 0.49], k2 ~ [-0.09 0.06] total integrated curvature = 0.587*4pi (7.375) --> 0 handles ICI = 1.6, FI = 11.5, variation=189.750 142 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 134 vertices thresholded to be in [-0.13 0.25] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.026 done. #----------------------------------------- #@# Curvature Stats rh Fri May 20 09:00:24 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm good_output rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ good_output/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 199 ] Gb_filter = 0 WARN: S lookup min: -0.332562 WARN: S explicit min: 0.000000 vertex = 83 #-------------------------------------------- #@# Sphere rh Fri May 20 09:00:33 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 0.95 hours scaling brain by 0.293... pass 1: epoch 1 of 3 starting distance error %18.93 pass 1: epoch 2 of 3 starting distance error %18.94 unfolding complete - removing small folds... starting distance error %18.87 removing remaining folds... final distance error %18.89 #-------------------------------------------- #@# Surf Reg rh Fri May 20 09:57:44 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_register -curv ../surf/rh.sphere /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.575 curvature mean = 0.043, std = 0.938 curvature mean = 0.019, std = 0.866 curvature mean = 0.025, std = 0.954 curvature mean = 0.008, std = 0.946 curvature mean = 0.020, std = 0.964 curvature mean = 0.004, std = 0.976 curvature mean = 0.018, std = 0.965 curvature mean = 0.001, std = 0.990 curvature mean = -0.025, std = 0.269 curvature mean = 0.006, std = 0.071 curvature mean = 0.063, std = 0.378 curvature mean = 0.005, std = 0.085 curvature mean = 0.029, std = 0.579 curvature mean = 0.006, std = 0.092 curvature mean = 0.016, std = 0.717 curvature mean = 0.006, std = 0.096 curvature mean = 0.005, std = 0.822 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri May 20 10:35:37 EDT 2011 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Fri May 20 10:35:40 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mrisp_paint -a 5 /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri May 20 10:35:43 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1047 labels changed using aseg relabeling using gibbs priors... 000: 2746 changed, 125936 examined... 001: 650 changed, 11779 examined... 002: 162 changed, 3623 examined... 003: 44 changed, 958 examined... 004: 17 changed, 258 examined... 005: 3 changed, 99 examined... 006: 0 changed, 16 examined... 141 labels changed using aseg 000: 93 total segments, 55 labels (354 vertices) changed 001: 41 total segments, 3 labels (3 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1700 vertices marked for relabeling... 1700 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 55 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri May 20 10:36:38 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs good_output rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11215 bright wm thresholded. 4651 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig... computing class statistics... border white: 235426 voxels (1.40%) border gray 265557 voxels (1.58%) WM (92.0): 92.8 +- 9.0 [70.0 --> 110.0] GM (77.0) : 75.3 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.4 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 37.8 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.3 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=63 using class modes intead of means.... mean inside = 91.5, mean outside = 71.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->2.94) (max @ vno 104941 --> 105650) face area 0.28 +- 0.12 (0.00-->1.39) mean absolute distance = 0.85 +- 1.07 3180 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 416 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown mean border=74.1, 79 (79) missing vertices, mean dist 0.4 [0.9 (%26.3)->0.8 (%73.7))] %49 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.10-->3.74) (max @ vno 94138 --> 95060) face area 0.28 +- 0.14 (0.00-->1.92) mean absolute distance = 0.41 +- 0.75 2954 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5815102.0, rms=12.35 001: dt: 0.5000, sse=5853526.5, rms=9.14 002: dt: 0.5000, sse=6040239.5, rms=7.09 003: dt: 0.5000, sse=6300629.0, rms=5.69 004: dt: 0.5000, sse=6416002.5, rms=4.79 005: dt: 0.5000, sse=6610877.5, rms=4.24 006: dt: 0.5000, sse=6702196.0, rms=3.95 007: dt: 0.5000, sse=6810444.5, rms=3.77 008: dt: 0.5000, sse=6819312.5, rms=3.69 009: dt: 0.5000, sse=6857430.5, rms=3.61 rms = 3.59, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6849787.5, rms=3.59 011: dt: 0.2500, sse=4153146.2, rms=2.39 012: dt: 0.2500, sse=3750070.8, rms=2.05 013: dt: 0.2500, sse=3571460.0, rms=1.96 014: dt: 0.2500, sse=3510275.0, rms=1.90 rms = 1.88, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3474266.0, rms=1.88 016: dt: 0.1250, sse=3402927.5, rms=1.82 rms = 1.81, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3384892.8, rms=1.81 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 3 with 361 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 7 with 9 points - only 11.11% unknown mean border=77.6, 40 (10) missing vertices, mean dist -0.3 [0.5 (%71.1)->0.3 (%28.9))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.08-->4.31) (max @ vno 51216 --> 52434) face area 0.36 +- 0.17 (0.00-->2.49) mean absolute distance = 0.31 +- 0.46 2914 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4076140.8, rms=5.20 018: dt: 0.5000, sse=4363448.0, rms=3.24 rms = 3.40, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=4009087.0, rms=2.51 020: dt: 0.2500, sse=3834047.8, rms=1.95 021: dt: 0.2500, sse=3712092.2, rms=1.69 022: dt: 0.2500, sse=3665886.0, rms=1.60 rms = 1.56, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3630028.0, rms=1.56 024: dt: 0.1250, sse=3585363.0, rms=1.51 rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3563772.8, rms=1.50 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 340 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown mean border=81.1, 50 (4) missing vertices, mean dist -0.2 [0.3 (%73.8)->0.2 (%26.2))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.06-->4.56) (max @ vno 51216 --> 52434) face area 0.35 +- 0.16 (0.00-->2.48) mean absolute distance = 0.24 +- 0.34 2705 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3953055.0, rms=4.39 026: dt: 0.5000, sse=4174623.2, rms=2.96 rms = 3.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3869013.2, rms=2.02 028: dt: 0.2500, sse=3756721.8, rms=1.56 029: dt: 0.2500, sse=3727533.0, rms=1.38 rms = 1.38, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3711411.2, rms=1.38 031: dt: 0.1250, sse=3669908.8, rms=1.32 rms = 1.33, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3669908.8, rms=1.32 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 407 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown mean border=82.4, 55 (2) missing vertices, mean dist -0.1 [0.3 (%59.5)->0.2 (%40.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3720921.0, rms=2.12 rms = 2.23, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3783073.0, rms=1.44 034: dt: 0.2500, sse=3932208.2, rms=1.01 rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3929960.5, rms=1.00 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=53.0, 75 (75) missing vertices, mean dist 1.8 [6.3 (%0.0)->2.1 (%100.0))] %24 local maxima, %62 large gradients and %10 min vals, 907 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=22653424.0, rms=29.09 001: dt: 0.5000, sse=16766929.0, rms=24.49 002: dt: 0.5000, sse=12489907.0, rms=20.54 003: dt: 0.5000, sse=9613295.0, rms=17.29 004: dt: 0.5000, sse=8099225.0, rms=14.63 005: dt: 0.5000, sse=7159759.5, rms=12.41 006: dt: 0.5000, sse=6573695.5, rms=10.58 007: dt: 0.5000, sse=6127641.0, rms=9.02 008: dt: 0.5000, sse=5909506.0, rms=7.66 009: dt: 0.5000, sse=5745183.5, rms=6.51 010: dt: 0.5000, sse=5764616.0, rms=5.57 011: dt: 0.5000, sse=5774315.5, rms=4.90 012: dt: 0.5000, sse=5890079.0, rms=4.46 013: dt: 0.5000, sse=5949190.0, rms=4.18 014: dt: 0.5000, sse=6032152.5, rms=4.02 015: dt: 0.5000, sse=6032331.5, rms=3.93 016: dt: 0.5000, sse=6090142.5, rms=3.86 rms = 3.81, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6070941.5, rms=3.81 018: dt: 0.2500, sse=4049065.0, rms=2.95 019: dt: 0.2500, sse=3798599.5, rms=2.72 rms = 2.67, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3674128.5, rms=2.67 021: dt: 0.1250, sse=3547484.5, rms=2.57 rms = 2.57, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3529126.0, rms=2.57 positioning took 2.2 minutes mean border=49.7, 328 (4) missing vertices, mean dist 0.2 [0.2 (%43.8)->0.6 (%56.2))] %49 local maxima, %40 large gradients and % 6 min vals, 243 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4392607.0, rms=5.87 023: dt: 0.5000, sse=4452891.0, rms=4.28 024: dt: 0.5000, sse=5518534.5, rms=3.98 rms = 3.96, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=5807424.5, rms=3.96 026: dt: 0.2500, sse=4414058.5, rms=2.96 027: dt: 0.2500, sse=4260705.0, rms=2.67 rms = 2.62, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4155466.8, rms=2.62 029: dt: 0.1250, sse=4028670.2, rms=2.50 rms = 2.48, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4008694.2, rms=2.48 positioning took 0.7 minutes mean border=46.9, 437 (4) missing vertices, mean dist 0.2 [0.2 (%37.4)->0.4 (%62.6))] %66 local maxima, %23 large gradients and % 6 min vals, 295 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4337409.5, rms=4.30 031: dt: 0.5000, sse=4437724.5, rms=3.74 rms = 3.76, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4156006.2, rms=2.92 033: dt: 0.2500, sse=4236153.0, rms=2.56 034: dt: 0.2500, sse=4223167.5, rms=2.48 rms = 2.44, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4234063.0, rms=2.44 036: dt: 0.1250, sse=4117151.8, rms=2.34 rms = 2.33, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4103950.0, rms=2.33 positioning took 0.7 minutes mean border=45.5, 855 (3) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.3 (%55.9))] %73 local maxima, %16 large gradients and % 5 min vals, 248 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4173440.2, rms=2.88 rms = 3.35, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4049674.5, rms=2.47 039: dt: 0.2500, sse=4108358.2, rms=2.30 040: dt: 0.2500, sse=4160440.5, rms=2.22 rms = 2.19, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4216832.0, rms=2.19 042: dt: 0.1250, sse=4129583.0, rms=2.12 rms = 2.11, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4127861.5, rms=2.11 positioning took 0.6 minutes writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.area.pial vertex spacing 1.02 +- 0.41 (0.04-->7.60) (max @ vno 95048 --> 94128) face area 0.41 +- 0.29 (0.00-->5.81) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 125936 vertices processed 25000 of 125936 vertices processed 50000 of 125936 vertices processed 75000 of 125936 vertices processed 100000 of 125936 vertices processed 125000 of 125936 vertices processed 0 of 125936 vertices processed 25000 of 125936 vertices processed 50000 of 125936 vertices processed 75000 of 125936 vertices processed 100000 of 125936 vertices processed 125000 of 125936 vertices processed thickness calculation complete, 262:547 truncations. 61569 vertices at 0 distance 81994 vertices at 1 distance 62631 vertices at 2 distance 21833 vertices at 3 distance 6683 vertices at 4 distance 2266 vertices at 5 distance 939 vertices at 6 distance 460 vertices at 7 distance 234 vertices at 8 distance 143 vertices at 9 distance 82 vertices at 10 distance 53 vertices at 11 distance 31 vertices at 12 distance 29 vertices at 13 distance 26 vertices at 14 distance 13 vertices at 15 distance 9 vertices at 16 distance 7 vertices at 17 distance 3 vertices at 18 distance 4 vertices at 19 distance 5 vertices at 20 distance writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.thickness positioning took 11.0 minutes #-------------------------------------------- #@# Surf Volume rh Fri May 20 10:47:40 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Fri May 20 10:47:41 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab good_output rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1334 910 2421 2.613 0.520 0.120 0.037 12 2.0 bankssts 974 665 1819 2.598 0.586 0.163 0.075 37 2.5 caudalanteriorcingulate 3054 2131 5888 2.474 0.500 0.133 0.046 35 5.9 caudalmiddlefrontal 1996 1286 2513 1.757 0.447 0.171 0.076 46 6.7 cuneus 575 407 1741 2.983 0.792 0.144 0.042 8 0.9 entorhinal 4752 3327 8621 2.248 0.686 0.145 0.045 75 9.2 fusiform 8071 5656 15040 2.343 0.612 0.152 0.058 130 19.8 inferiorparietal 4214 2906 8708 2.460 0.746 0.144 0.052 69 8.7 inferiortemporal 1296 823 2039 2.358 0.859 0.152 0.061 29 3.6 isthmuscingulate 6229 4230 9811 2.069 0.533 0.161 0.064 124 15.6 lateraloccipital 3772 2572 6644 2.299 0.704 0.144 0.055 60 8.4 lateralorbitofrontal 3688 2599 4966 1.751 0.500 0.149 0.048 51 7.5 lingual 2913 2037 5378 2.239 0.689 0.153 0.070 73 7.7 medialorbitofrontal 5034 3541 11226 2.635 0.650 0.148 0.060 92 11.9 middletemporal 1120 744 2117 2.304 0.902 0.108 0.081 27 1.3 parahippocampal 2367 1547 3555 2.117 0.547 0.120 0.039 22 4.0 paracentral 2236 1517 4236 2.475 0.496 0.135 0.041 29 3.7 parsopercularis 1091 721 2239 2.504 0.472 0.159 0.067 21 2.8 parsorbitalis 1814 1254 3635 2.513 0.516 0.147 0.053 28 4.0 parstriangularis 1591 1071 1631 1.537 0.348 0.136 0.043 17 2.9 pericalcarine 5092 3412 7278 1.882 0.621 0.127 0.038 86 8.0 postcentral 1732 1204 3334 2.485 0.594 0.156 0.053 34 3.7 posteriorcingulate 7030 4467 12136 2.472 0.583 0.119 0.043 78 11.7 precentral 5694 3856 9312 2.210 0.641 0.151 0.060 95 14.2 precuneus 671 448 1394 2.604 0.671 0.126 0.054 13 1.6 rostralanteriorcingulate 7098 4969 13330 2.280 0.597 0.149 0.060 125 16.4 rostralmiddlefrontal 8598 5949 17157 2.483 0.577 0.147 0.060 210 22.0 superiorfrontal 7574 5025 11311 2.031 0.519 0.132 0.042 87 13.0 superiorparietal 5199 3556 10218 2.513 0.646 0.134 0.049 126 9.3 superiortemporal 5654 3783 10041 2.353 0.585 0.136 0.050 100 11.7 supramarginal 282 188 739 2.678 0.572 0.199 0.091 8 1.2 frontalpole 422 330 1791 3.686 0.428 0.155 0.065 6 1.1 temporalpole 558 330 772 2.072 0.360 0.130 0.042 7 0.9 transversetemporal 3653 2404 7178 2.764 0.867 0.129 0.065 58 8.8 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri May 20 10:47:57 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 26 labels changed using aseg relabeling using gibbs priors... 000: 9088 changed, 125936 examined... 001: 2155 changed, 34776 examined... 002: 646 changed, 11318 examined... 003: 267 changed, 3654 examined... 004: 130 changed, 1506 examined... 005: 58 changed, 741 examined... 006: 50 changed, 356 examined... 007: 35 changed, 259 examined... 008: 17 changed, 193 examined... 009: 9 changed, 94 examined... 010: 3 changed, 48 examined... 011: 3 changed, 15 examined... 012: 0 changed, 17 examined... 15 labels changed using aseg 000: 252 total segments, 167 labels (1936 vertices) changed 001: 93 total segments, 8 labels (39 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 135 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1125 vertices marked for relabeling... 1125 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 56 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri May 20 10:48:54 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab good_output rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 723 509 1344 2.213 0.588 0.170 0.060 15 1.9 G_and_S_frontomargin 1350 927 2760 2.486 0.623 0.167 0.072 41 3.1 G_and_S_occipital_inf 1290 842 2017 1.990 0.521 0.133 0.045 14 2.5 G_and_S_paracentral 1231 828 2548 2.527 0.581 0.146 0.050 49 2.5 G_and_S_subcentral 945 657 1793 2.149 0.615 0.160 0.065 21 2.6 G_and_S_transv_frontopol 2483 1714 4628 2.429 0.585 0.133 0.046 39 4.7 G_and_S_cingul-Ant 1205 852 2227 2.333 0.538 0.143 0.055 20 2.7 G_and_S_cingul-Mid-Ant 1260 867 2247 2.340 0.548 0.127 0.041 14 2.0 G_and_S_cingul-Mid-Post 592 383 1426 2.824 0.490 0.191 0.068 16 1.7 G_cingul-Post-dorsal 245 169 489 2.696 0.790 0.157 0.078 4 0.5 G_cingul-Post-ventral 1904 1212 2483 1.773 0.435 0.174 0.080 47 7.1 G_cuneus 1242 826 2889 2.676 0.496 0.156 0.055 24 2.7 G_front_inf-Opercular 195 132 472 2.727 0.338 0.171 0.104 6 0.6 G_front_inf-Orbital 949 663 2380 2.711 0.487 0.154 0.061 18 2.3 G_front_inf-Triangul 3720 2644 8578 2.522 0.559 0.160 0.069 80 10.0 G_front_middle 6130 4151 13599 2.626 0.564 0.165 0.076 197 20.0 G_front_sup 530 360 1269 2.977 0.834 0.123 0.063 10 1.1 G_Ins_lg_and_S_cent_ins 557 379 1805 3.470 0.745 0.186 0.089 15 1.8 G_insular_short 1927 1351 4037 2.416 0.530 0.175 0.077 42 7.5 G_occipital_middle 1647 1095 2616 2.075 0.592 0.148 0.052 24 3.4 G_occipital_sup 1887 1319 3982 2.475 0.553 0.150 0.053 36 4.3 G_oc-temp_lat-fusifor 2238 1541 3250 1.803 0.551 0.155 0.055 33 5.1 G_oc-temp_med-Lingual 1861 1230 4513 2.811 0.894 0.143 0.105 54 5.0 G_oc-temp_med-Parahip 2726 1856 6065 2.512 0.721 0.163 0.066 55 7.3 G_orbital 3098 2168 7329 2.616 0.623 0.183 0.083 77 10.2 G_pariet_inf-Angular 2990 2006 6103 2.505 0.554 0.150 0.060 52 7.7 G_pariet_inf-Supramar 2248 1501 4082 2.197 0.479 0.141 0.044 31 4.1 G_parietal_sup 1917 1249 2947 1.948 0.521 0.131 0.041 23 3.3 G_postcentral 2704 1636 5769 2.720 0.470 0.132 0.066 48 6.2 G_precentral 2818 1884 5562 2.412 0.612 0.168 0.081 68 9.6 G_precuneus 781 588 1994 2.556 0.484 0.217 0.137 36 3.7 G_rectus 368 228 589 2.417 0.699 0.129 0.085 7 1.6 G_subcallosal 447 261 702 2.200 0.371 0.146 0.073 53 0.9 G_temp_sup-G_T_transv 1888 1278 4843 2.819 0.634 0.160 0.070 45 5.1 G_temp_sup-Lateral 760 539 1568 2.597 0.723 0.095 0.024 3 0.8 G_temp_sup-Plan_polar 766 505 1326 2.319 0.533 0.121 0.040 31 1.4 G_temp_sup-Plan_tempo 2557 1800 6309 2.623 0.729 0.171 0.070 59 7.3 G_temporal_inf 3032 2167 7834 2.776 0.634 0.168 0.079 74 9.3 G_temporal_middle 387 255 550 2.322 0.424 0.115 0.024 3 0.4 Lat_Fis-ant-Horizont 137 93 226 2.362 0.624 0.138 0.029 1 0.2 Lat_Fis-ant-Vertical 1363 909 1819 2.307 0.544 0.109 0.027 8 1.5 Lat_Fis-post 2898 1969 4337 1.868 0.463 0.174 0.067 56 7.6 Pole_occipital 1461 1020 4432 3.073 0.748 0.162 0.065 34 3.8 Pole_temporal 1577 1076 1799 1.822 0.670 0.131 0.036 15 2.3 S_calcarine 3018 1991 3459 1.898 0.718 0.106 0.027 18 3.5 S_central 1370 959 1859 2.005 0.522 0.110 0.029 9 1.7 S_cingul-Marginalis 690 455 1052 2.553 0.748 0.111 0.032 4 0.9 S_circular_insula_ant 1212 774 1556 2.228 0.626 0.079 0.018 4 0.9 S_circular_insula_inf 1318 895 1957 2.356 0.468 0.117 0.030 9 1.6 S_circular_insula_sup 970 681 1226 1.807 0.628 0.110 0.022 6 0.9 S_collat_transv_ant 617 414 649 1.767 0.360 0.134 0.044 6 1.1 S_collat_transv_post 2479 1671 3747 2.239 0.450 0.127 0.040 27 3.8 S_front_inf 1268 906 2305 2.244 0.654 0.137 0.053 16 3.0 S_front_middle 2170 1524 3275 2.176 0.500 0.114 0.029 15 2.8 S_front_sup 833 551 1110 2.043 0.426 0.111 0.030 6 1.0 S_interm_prim-Jensen 3162 2125 3723 1.869 0.438 0.116 0.031 24 4.1 S_intrapariet_and_P_trans 926 625 1169 1.867 0.398 0.132 0.040 10 1.5 S_oc_middle_and_Lunatus 1626 1100 1979 1.892 0.435 0.116 0.033 12 2.1 S_oc_sup_and_transversal 529 357 715 2.252 0.384 0.117 0.033 4 0.7 S_occipital_ant 880 609 1130 2.093 0.534 0.136 0.039 10 1.4 S_oc-temp_lat 2075 1504 2537 1.701 0.512 0.117 0.027 18 2.3 S_oc-temp_med_and_Lingual 441 299 659 2.091 0.505 0.126 0.079 5 0.7 S_orbital_lateral 956 663 1225 1.818 0.656 0.103 0.024 6 1.0 S_orbital_med-olfact 1271 862 2042 2.330 0.617 0.141 0.056 20 3.0 S_orbital-H_Shaped 2157 1436 2465 1.886 0.597 0.144 0.047 26 4.3 S_parieto_occipital 1383 866 1546 2.308 0.838 0.157 0.068 56 3.9 S_pericallosal 1668 1122 2016 1.848 0.567 0.113 0.029 12 2.0 S_postcentral 1580 1080 2327 2.270 0.390 0.111 0.028 10 1.9 S_precentral-inf-part 1035 715 1457 2.311 0.471 0.115 0.028 7 1.3 S_precentral-sup-part 485 324 569 1.749 0.649 0.106 0.026 3 0.5 S_suborbital 973 675 1575 2.136 0.508 0.135 0.041 11 1.6 S_subparietal 1231 830 1809 2.466 0.557 0.129 0.038 11 1.9 S_temporal_inf 5769 4014 9216 2.338 0.559 0.119 0.033 52 7.4 S_temporal_sup 252 196 326 1.841 0.407 0.156 0.037 3 0.4 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Fri May 20 10:49:12 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon good_output SUBJECTS_DIR is /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 26 writing volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri May 20 11:03:53 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /space/freesurfer/centos4.0_x86_64/stable5/ASegStatsLUT.txt --subject good_output $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /space/freesurfer/centos4.0_x86_64/stable5/ASegStatsLUT.txt --subject good_output sysname Linux hostname compute-0-2.local machine x86_64 user khoa atlas_icv (eTIV) = 1513067 mm^3 (det: 1.287521 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 218095 rh white matter volume 223822 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 250504.357128, pTot = 455029.734052 c = 204525.376924 rh surface-based volumes (mm3): wTot = 257296.843530, pTot = 461697.656356 c = 204400.812825 Computing SupraTentVolCor SupraTentVolCor = 62525.000 SupraTentVol = 979252.390 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 16998 16998 4 5 Left-Inf-Lat-Vent 831 831 5 7 Left-Cerebellum-White-Matter 11210 11210 6 8 Left-Cerebellum-Cortex 40795 40795 7 10 Left-Thalamus-Proper 6191 6191 8 11 Left-Caudate 5260 5260 9 12 Left-Putamen 5586 5586 10 13 Left-Pallidum 1642 1642 11 14 3rd-Ventricle 1546 1546 12 15 4th-Ventricle 2027 2027 13 16 Brain-Stem 17861 17861 14 17 Left-Hippocampus 3997 3997 15 18 Left-Amygdala 1274 1274 16 24 CSF 1047 1047 17 26 Left-Accumbens-area 525 525 18 28 Left-VentralDC 3043 3043 19 30 Left-vessel 91 91 20 31 Left-choroid-plexus 2039 2039 23 43 Right-Lateral-Ventricle 19994 19994 24 44 Right-Inf-Lat-Vent 944 944 25 46 Right-Cerebellum-White-Matter 11086 11086 26 47 Right-Cerebellum-Cortex 42205 42205 27 49 Right-Thalamus-Proper 5922 5922 28 50 Right-Caudate 4850 4850 29 51 Right-Putamen 5290 5290 30 52 Right-Pallidum 1436 1436 31 53 Right-Hippocampus 4108 4108 32 54 Right-Amygdala 1489 1489 33 58 Right-Accumbens-area 681 681 34 60 Right-VentralDC 3337 3337 35 62 Right-vessel 113 113 36 63 Right-choroid-plexus 2271 2271 37 72 5th-Ventricle 49 49 38 77 WM-hypointensities 4615 4615 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 109 109 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 340 340 45 251 CC_Posterior 957 957 46 252 CC_Mid_Posterior 266 266 47 253 CC_Central 346 346 48 254 CC_Mid_Anterior 337 337 49 255 CC_Anterior 713 713 Reporting on 45 segmentations SubCortGrayVol = 155492 #----------------------------------------- #@# AParc-to-ASeg Fri May 20 11:15:29 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_aparc2aseg --s good_output --volmask SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output outvol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 402514 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_aparc2aseg --s good_output --volmask --a2009s SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output outvol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 402514 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri May 20 11:18:35 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_aparc2aseg --s good_output --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz Loading filled from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8335 vertices from left hemi Ripped 8558 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz Loading Ctx Seg File /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 820636 Used brute-force search on 221 voxels Fixing Parahip LH WM Found 15 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 10.000000 4 k 2.000000 5 k 1452.000000 6 k 2.000000 7 k 4.000000 8 k 1.000000 9 k 1.000000 10 k 2.000000 11 k 1.000000 12 k 1.000000 13 k 6.000000 14 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1617.000000 6 k 31.000000 7 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject good_output --surf-wm-vol --ctab /space/freesurfer/centos4.0_x86_64/stable5/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject good_output --surf-wm-vol --ctab /space/freesurfer/centos4.0_x86_64/stable5/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-2.local machine x86_64 user khoa atlas_icv (eTIV) = 1513067 mm^3 (det: 1.287521 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 218095 rh white matter volume 223822 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1536801 # brainmaskvolume 1536801.0 # nbrainsegvoxels 226599 # brainsegvolume 226599.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 3675 3675 2 3002 wm-lh-caudalanteriorcingulate 3077 3077 3 3003 wm-lh-caudalmiddlefrontal 6109 6109 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 1698 1698 6 3006 wm-lh-entorhinal 778 778 7 3007 wm-lh-fusiform 6593 6593 8 3008 wm-lh-inferiorparietal 9378 9378 9 3009 wm-lh-inferiortemporal 6133 6133 10 3010 wm-lh-isthmuscingulate 3747 3747 11 3011 wm-lh-lateraloccipital 7045 7045 12 3012 wm-lh-lateralorbitofrontal 5548 5548 13 3013 wm-lh-lingual 4516 4516 14 3014 wm-lh-medialorbitofrontal 4718 4718 15 3015 wm-lh-middletemporal 5514 5514 16 3016 wm-lh-parahippocampal 1561 1561 17 3017 wm-lh-paracentral 3575 3575 18 3018 wm-lh-parsopercularis 3036 3036 19 3019 wm-lh-parsorbitalis 960 960 20 3020 wm-lh-parstriangularis 2392 2392 21 3021 wm-lh-pericalcarine 1915 1915 22 3022 wm-lh-postcentral 7419 7419 23 3023 wm-lh-posteriorcingulate 4065 4065 24 3024 wm-lh-precentral 11620 11620 25 3025 wm-lh-precuneus 8591 8591 26 3026 wm-lh-rostralanteriorcingulate 2274 2274 27 3027 wm-lh-rostralmiddlefrontal 10878 10878 28 3028 wm-lh-superiorfrontal 15504 15504 29 3029 wm-lh-superiorparietal 11780 11780 30 3030 wm-lh-superiortemporal 7379 7379 31 3031 wm-lh-supramarginal 9448 9448 32 3032 wm-lh-frontalpole 219 219 33 3033 wm-lh-temporalpole 712 712 34 3034 wm-lh-transversetemporal 702 702 35 3035 wm-lh-insula 9162 9162 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2893 2893 120 4002 wm-rh-caudalanteriorcingulate 2658 2658 121 4003 wm-rh-caudalmiddlefrontal 6301 6301 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1910 1910 124 4006 wm-rh-entorhinal 835 835 125 4007 wm-rh-fusiform 6823 6823 126 4008 wm-rh-inferiorparietal 12682 12682 127 4009 wm-rh-inferiortemporal 4950 4950 128 4010 wm-rh-isthmuscingulate 3462 3462 129 4011 wm-rh-lateraloccipital 8055 8055 130 4012 wm-rh-lateralorbitofrontal 6182 6182 131 4013 wm-rh-lingual 4228 4228 132 4014 wm-rh-medialorbitofrontal 3571 3571 133 4015 wm-rh-middletemporal 6491 6491 134 4016 wm-rh-parahippocampal 1745 1745 135 4017 wm-rh-paracentral 4648 4648 136 4018 wm-rh-parsopercularis 3658 3658 137 4019 wm-rh-parsorbitalis 1035 1035 138 4020 wm-rh-parstriangularis 2698 2698 139 4021 wm-rh-pericalcarine 2033 2033 140 4022 wm-rh-postcentral 6135 6135 141 4023 wm-rh-posteriorcingulate 4183 4183 142 4024 wm-rh-precentral 12679 12679 143 4025 wm-rh-precuneus 9358 9358 144 4026 wm-rh-rostralanteriorcingulate 1753 1753 145 4027 wm-rh-rostralmiddlefrontal 10930 10930 146 4028 wm-rh-superiorfrontal 15080 15080 147 4029 wm-rh-superiorparietal 11530 11530 148 4030 wm-rh-superiortemporal 6462 6462 149 4031 wm-rh-supramarginal 9164 9164 150 4032 wm-rh-frontalpole 185 185 151 4033 wm-rh-temporalpole 498 498 152 4034 wm-rh-transversetemporal 535 535 153 4035 wm-rh-insula 9283 9283 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 25080 25080 237 5002 Right-UnsegmentedWhiteMatter 26283 26283 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label #-------------------------------------------- #@# BA Labels lh Fri May 20 11:39:02 EDT 2011 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA1.label --trgsubject good_output --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 351 Checking for and removing duplicates Writing label file ./lh.BA1.label 4480 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA2.label --trgsubject good_output --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 827 Checking for and removing duplicates Writing label file ./lh.BA2.label 8736 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3a.label --trgsubject good_output --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4215 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3b.label --trgsubject good_output --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 411 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6394 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4a.label --trgsubject good_output --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6028 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4p.label --trgsubject good_output --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4252 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA6.label --trgsubject good_output --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 613 Checking for and removing duplicates Writing label file ./lh.BA6.label 14202 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA44.label --trgsubject good_output --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./lh.BA44.label 4500 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA45.label --trgsubject good_output --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 506 Checking for and removing duplicates Writing label file ./lh.BA45.label 3928 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V1.label --trgsubject good_output --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 543 Checking for and removing duplicates Writing label file ./lh.V1.label 5184 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V2.label --trgsubject good_output --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 1846 Checking for and removing duplicates Writing label file ./lh.V2.label 9960 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.MT.label --trgsubject good_output --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./lh.MT.label 2215 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s good_output --hemi lh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose Reading ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label cmdline mris_label2annot --s good_output --hemi lh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-2.local machine x86_64 user khoa subject good_output hemi lh SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs ColorTable /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 88679 unhit vertices Writing annot to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab good_output lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1068 647 1661 2.025 0.488 0.156 0.059 19 2.8 BA1 4228 2811 6538 2.164 0.512 0.135 0.048 56 8.8 BA2 942 656 898 1.728 0.373 0.126 0.034 7 1.3 BA3a 2601 1757 3647 1.825 0.573 0.128 0.045 32 4.7 BA3b 1529 945 2661 2.469 0.498 0.117 0.044 14 2.9 BA4a 1352 820 2016 2.493 0.498 0.104 0.037 10 2.3 BA4p 7417 5085 15708 2.643 0.567 0.140 0.063 127 20.0 BA6 2369 1629 4240 2.332 0.455 0.135 0.044 32 4.1 BA44 2692 1905 5084 2.252 0.473 0.160 0.068 53 7.4 BA45 2368 1639 2705 1.554 0.416 0.151 0.059 37 5.8 V1 6960 4751 9564 1.835 0.550 0.157 0.059 161 16.3 V2 1605 1093 2514 2.143 0.467 0.136 0.042 20 2.9 MT #-------------------------------------------- #@# BA Labels rh Fri May 20 11:41:26 EDT 2011 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA1.label --trgsubject good_output --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./rh.BA1.label 4078 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA2.label --trgsubject good_output --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.BA2.label 6805 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3a.label --trgsubject good_output --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 151 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4131 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3b.label --trgsubject good_output --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 199 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4721 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4a.label --trgsubject good_output --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 286 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6033 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4p.label --trgsubject good_output --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4705 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA6.label --trgsubject good_output --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 635 Checking for and removing duplicates Writing label file ./rh.BA6.label 12891 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA44.label --trgsubject good_output --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 899 Checking for and removing duplicates Writing label file ./rh.BA44.label 7811 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA45.label --trgsubject good_output --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 928 Checking for and removing duplicates Writing label file ./rh.BA45.label 6283 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V1.label --trgsubject good_output --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 760 Checking for and removing duplicates Writing label file ./rh.V1.label 5487 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V2.label --trgsubject good_output --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 2155 Checking for and removing duplicates Writing label file ./rh.V2.label 10171 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.MT.label --trgsubject good_output --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./rh.MT.label 2148 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s good_output --hemi rh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose Reading ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label cmdline mris_label2annot --s good_output --hemi rh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-2.local machine x86_64 user khoa subject good_output hemi rh SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs ColorTable /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 90256 unhit vertices Writing annot to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab good_output rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 741 409 1296 2.267 0.446 0.151 0.059 13 1.8 BA1 2457 1708 3524 1.937 0.577 0.117 0.031 19 3.2 BA2 1033 697 920 1.556 0.433 0.118 0.031 7 1.4 BA3a 1931 1329 2469 1.613 0.527 0.127 0.039 51 3.2 BA3b 1520 930 2697 2.492 0.601 0.116 0.063 17 2.8 BA4a 1349 821 2136 2.584 0.622 0.104 0.033 18 2.0 BA4p 6862 4532 13730 2.579 0.524 0.142 0.058 172 18.1 BA6 3835 2578 6636 2.394 0.495 0.127 0.037 41 5.9 BA44 4103 2806 8120 2.436 0.496 0.149 0.061 68 9.5 BA45 2846 1934 3511 1.637 0.444 0.156 0.055 45 6.4 V1 7419 4995 10179 1.873 0.500 0.158 0.060 125 18.3 V2 1584 1125 2868 2.261 0.566 0.160 0.060 28 4.6 MT /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri May 20 11:43:48 EDT 2011 mris_spherical_average -erode 1 -orig white -t 0.4 -o good_output label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject good_output. processing subject lh.EC_average... reading output surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 850 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label good_output lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 300 199 1115 3.330 0.555 0.156 0.051 9 0.8 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri May 20 11:44:07 EDT 2011 mris_spherical_average -erode 1 -orig white -t 0.4 -o good_output label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject good_output. processing subject rh.EC_average... reading output surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 824 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label good_output rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 315 200 1015 3.177 0.611 0.127 0.057 4 0.9 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s good_output finished without error at Fri May 20 11:44:26 EDT 2011 New invocation of recon-all Sat May 21 10:23:46 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output /space/freesurfer/centos4.0_x86_64/stable5/bin/recon-all -skullstrip -gcut -s good_output/ subjid good_output setenv SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110521 Linux dharma 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 137216 total used free shared buffers cached Mem: 16438368 13653492 2784876 0 282456 11730436 -/+ buffers/cache: 1640600 14797768 Swap: 16386260 220 16386040 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:47-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:48-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:49-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:50-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:50-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:51-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:52-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:52-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:53-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:54-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:55-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:56-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:56-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:57-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:23:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:01-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:01-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:02-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:03-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:03-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:04-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:05-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:05-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:06-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:07-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:08-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:08-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:09-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:10-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:10-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:11-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:12-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:12-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:13-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:24:14-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: khoa Machine: dharma Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /space/freesurfer/centos4.0_x86_64/stable5/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /space/freesurfer/centos4.0_x86_64/stable5/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Skull Stripping Sat May 21 10:24:14 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading extra input line fscale 0.150000 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=103 z=121 r=82 first estimation of the main basin volume: 2310299 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=108, y=87, z=83, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=31418272875 voxels, voxel volume =1.000 = 31418272875 mmm3 = 31418273.792 cm3 done. PostAnalyze...Basin Prior 93 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=110, z=114, r=10063 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 44748 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=20 , nb = 2880 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=17 , nb = 2502 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = 19314 LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=38 , nb = 19512 OTHER CSF_MIN=1, CSF_intensity=16, CSF_MAX=36 , nb = 540 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 32, 25, 58 after analyzing : 25, 32, 32, 38 RIGHT_CER before analyzing : 20, 28, 41, 68 after analyzing : 20, 36, 41, 44 LEFT_CER before analyzing : 17, 21, 33, 66 after analyzing : 17, 29, 33, 38 RIGHT_BRAIN before analyzing : 40, 32, 24, 59 after analyzing : 26, 32, 32, 38 LEFT_BRAIN before analyzing : 38, 31, 24, 59 after analyzing : 24, 31, 31, 38 OTHER before analyzing : 36, 65, 83, 95 after analyzing : 36, 77, 83, 81 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 68.714, std = 8.031 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.33, sigma = 3.35 after rotation: sse = 2.33, sigma = 3.35 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.39, its var is 3.00 before Erosion-Dilatation 0.13% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 1558341 voxels, voxel volume = 1.000 mm3 = 1558341 mmm3 = 1558.341 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done rm -f brainmask.gcuts.mgz mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed. reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.400000=44.000000 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... mri_binarize --i brainmask.gcuts.mgz --o brainmask.gcuts.mgz --binval 999 --min 1 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri cmdline mri_binarize --i brainmask.gcuts.mgz --o brainmask.gcuts.mgz --binval 999 --min 1 sysname Linux hostname dharma machine x86_64 user khoa input brainmask.gcuts.mgz frame 0 nErode3d 0 nErode2d 0 output brainmask.gcuts.mgz Binarizing based on threshold min 1 max +infinity binval 999 binvalnot 0 Found 169692 values in range Counting number of voxels Found 169692 voxels in final mask mri_binarize done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------------ recon-all -s good_output finished without error at Sat May 21 10:25:26 EDT 2011 New invocation of recon-all Sat May 21 10:26:46 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output /space/freesurfer/centos4.0_x86_64/stable5/bin/recon-all -autorecon2 -autorecon3 -s good_output/ subjid good_output setenv SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110521 Linux compute-0-1.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse 4194304 kbytes vmemoryuse 8388608 kbytes descriptors 4096 memorylocked 4194304 kbytes maxproc 268288 total used free shared buffers cached Mem: 32962780 5009320 27953460 0 163764 1571632 -/+ buffers/cache: 3273924 29688856 Swap: 32764556 443936 32320620 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:48-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:49-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:50-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:51-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:51-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:51-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:52-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:52-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:53-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:53-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:53-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:54-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:55-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:55-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:56-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:56-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:56-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:57-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:58-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:26:59-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:27:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:27:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:27:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:27:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:27:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/05/21-14:27:00-GMT BuildTimeStamp: May 21 2011 05:40:36 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: khoa Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /space/freesurfer/centos4.0_x86_64/stable5/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /space/freesurfer/centos4.0_x86_64/stable5/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Sat May 21 10:27:01 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (61, 50, 36) --> (194, 163, 203) using (105, 88, 120) as brain centroid... mean wm in atlas = 107, using box (89,74,99) --> (121, 101,140) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -7447.0 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, 8.5, -8.5): log p = -7128.690 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6995.3, old_max_log_p =-7128.7 (thresh=-7121.6) 1.064 0.000 0.000 -8.688; 0.000 1.226 0.140 -32.353; 0.000 -0.150 0.991 9.014; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6995.3, old_max_log_p =-6995.3 (thresh=-6988.3) 1.064 0.000 0.000 -8.688; 0.000 1.226 0.140 -32.353; 0.000 -0.150 0.991 9.014; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6903.9, old_max_log_p =-6995.3 (thresh=-6988.3) 1.043 0.000 0.000 -7.998; 0.000 1.256 0.077 -28.441; 0.000 -0.068 0.980 -2.362; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6884.0, old_max_log_p =-6903.9 (thresh=-6897.0) 1.062 0.000 0.000 -10.431; 0.000 1.253 0.109 -30.011; 0.000 -0.111 0.995 2.463; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6884.0, old_max_log_p =-6884.0 (thresh=-6877.2) 1.062 0.000 0.000 -10.431; 0.000 1.253 0.109 -30.011; 0.000 -0.111 0.995 2.463; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6846.0, old_max_log_p =-6884.0 (thresh=-6877.2) 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6846.0, old_max_log_p =-6846.0 (thresh=-6839.2) 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 6846.0 tol 0.000010 Resulting transform: 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -6846.0 (old=-7447.0) transform before final EM align: 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.06401 -0.03015 -0.01041 -6.23179; 0.02601 1.25288 0.09223 -31.92746; 0.00871 -0.09113 0.99548 -0.91893; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 832096.9 after pass:transform: ( 1.06, -0.03, -0.01, -6.23) ( 0.03, 1.25, 0.09, -31.93) ( 0.01, -0.09, 1.00, -0.92) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 832096.9 tol 0.000000 final transform: 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 24 minutes and 3 seconds. #-------------------------------------- #@# CA Normalize Sat May 21 10:51:05 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (61, 50, 37) --> (194, 163, 203) using (105, 88, 120) as brain centroid... mean wm in atlas = 107, using box (89,74,100) --> (121, 101,140) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (191, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 225.0 0 of 46 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (129, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 225.0 0 of 84 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (176, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 225.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 123, 59) --> (129, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 225.0 1 of 10 (10.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 118, 96) --> (145, 173, 127) Brain_Stem: limiting intensities to 87.0 --> 225.0 0 of 6 (0.0%) samples deleted using 157 total control points for intensity normalization... bias field = 0.995 +- 0.063 0 of 156 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (191, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 209.0 0 of 105 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (129, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 209.0 0 of 111 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (176, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 209.0 0 of 22 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 123, 59) --> (129, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 209.0 0 of 56 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 118, 96) --> (145, 173, 127) Brain_Stem: limiting intensities to 67.0 --> 209.0 0 of 82 (0.0%) samples deleted using 376 total control points for intensity normalization... bias field = 0.996 +- 0.044 0 of 376 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 37) --> (191, 148, 205) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 206.0 0 of 219 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 57, 37) --> (129, 149, 205) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 206.0 0 of 263 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 123, 61) --> (176, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 206.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 123, 59) --> (129, 159, 116) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 206.0 0 of 48 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 118, 96) --> (145, 173, 127) Brain_Stem: limiting intensities to 80.0 --> 206.0 29 of 136 (21.3%) samples deleted using 751 total control points for intensity normalization... bias field = 0.995 +- 0.038 0 of 722 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 57 seconds. #-------------------------------------- #@# CA Reg Sat May 21 10:53:03 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.34 (predicted orig area = 6.0) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.905, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37130.590 ms 0001: dt=129.472000, rms=0.852 (5.860%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37158.707 ms 0002: dt=129.472000, rms=0.820 (3.772%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37303.012 ms 0003: dt=110.976000, rms=0.815 (0.687%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47302.074 ms 0004: dt=295.936000, rms=0.797 (2.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37671.227 ms 0005: dt=32.368000, rms=0.793 (0.522%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39803.957 ms 0006: dt=55.488000, rms=0.791 (0.238%), neg=0, invalid=766 0007: dt=55.488000, rms=0.790 (0.184%), neg=0, invalid=766 0008: dt=55.488000, rms=0.787 (0.314%), neg=0, invalid=766 0009: dt=55.488000, rms=0.784 (0.452%), neg=0, invalid=766 0010: dt=55.488000, rms=0.780 (0.558%), neg=0, invalid=766 0011: dt=55.488000, rms=0.775 (0.588%), neg=0, invalid=766 0012: dt=55.488000, rms=0.771 (0.564%), neg=0, invalid=766 0013: dt=55.488000, rms=0.767 (0.496%), neg=0, invalid=766 0014: dt=55.488000, rms=0.764 (0.408%), neg=0, invalid=766 0015: dt=55.488000, rms=0.761 (0.382%), neg=0, invalid=766 0016: dt=55.488000, rms=0.758 (0.390%), neg=0, invalid=766 0017: dt=55.488000, rms=0.755 (0.411%), neg=0, invalid=766 0018: dt=55.488000, rms=0.752 (0.402%), neg=0, invalid=766 0019: dt=55.488000, rms=0.749 (0.379%), neg=0, invalid=766 0020: dt=55.488000, rms=0.746 (0.360%), neg=0, invalid=766 0021: dt=55.488000, rms=0.743 (0.352%), neg=0, invalid=766 0022: dt=55.488000, rms=0.741 (0.346%), neg=0, invalid=766 0023: dt=55.488000, rms=0.738 (0.334%), neg=0, invalid=766 0024: dt=55.488000, rms=0.736 (0.319%), neg=0, invalid=766 0025: dt=55.488000, rms=0.734 (0.298%), neg=0, invalid=766 0026: dt=55.488000, rms=0.732 (0.268%), neg=0, invalid=766 0027: dt=55.488000, rms=0.730 (0.265%), neg=0, invalid=766 0028: dt=55.488000, rms=0.728 (0.257%), neg=0, invalid=766 0029: dt=55.488000, rms=0.726 (0.243%), neg=0, invalid=766 0030: dt=55.488000, rms=0.724 (0.266%), neg=0, invalid=766 0031: dt=55.488000, rms=0.723 (0.238%), neg=0, invalid=766 0032: dt=55.488000, rms=0.721 (0.215%), neg=0, invalid=766 0033: dt=55.488000, rms=0.720 (0.193%), neg=0, invalid=766 0034: dt=55.488000, rms=0.718 (0.181%), neg=0, invalid=766 0035: dt=55.488000, rms=0.717 (0.176%), neg=0, invalid=766 0036: dt=55.488000, rms=0.716 (0.186%), neg=0, invalid=766 0037: dt=55.488000, rms=0.715 (0.175%), neg=0, invalid=766 0038: dt=55.488000, rms=0.713 (0.148%), neg=0, invalid=766 0039: dt=55.488000, rms=0.713 (0.126%), neg=0, invalid=766 0040: dt=55.488000, rms=0.712 (0.112%), neg=0, invalid=766 0041: dt=55.488000, rms=0.711 (0.122%), neg=0, invalid=766 0042: dt=55.488000, rms=0.710 (0.127%), neg=0, invalid=766 0043: dt=55.488000, rms=0.709 (0.130%), neg=0, invalid=766 0044: dt=55.488000, rms=0.708 (0.110%), neg=0, invalid=766 0045: dt=55.488000, rms=0.708 (0.079%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42073.234 ms 0046: dt=517.888000, rms=0.707 (0.042%), neg=0, invalid=766 0047: dt=517.888000, rms=0.707 (-0.310%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.707, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41556.125 ms 0048: dt=110.976000, rms=0.707 (0.065%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41557.426 ms 0049: dt=369.920000, rms=0.706 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45194.043 ms 0050: dt=129.472000, rms=0.706 (0.033%), neg=0, invalid=766 0051: dt=129.472000, rms=0.705 (0.054%), neg=0, invalid=766 0052: dt=129.472000, rms=0.705 (0.055%), neg=0, invalid=766 0053: dt=129.472000, rms=0.705 (0.061%), neg=0, invalid=766 0054: dt=129.472000, rms=0.704 (0.038%), neg=0, invalid=766 0055: dt=129.472000, rms=0.704 (0.013%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.711, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41863.859 ms 0056: dt=145.152000, rms=0.689 (3.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39158.504 ms 0057: dt=36.288000, rms=0.686 (0.459%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42191.414 ms 0058: dt=103.680000, rms=0.675 (1.708%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41214.930 ms 0059: dt=14.322581, rms=0.672 (0.408%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39700.043 ms 0060: dt=15.552000, rms=0.671 (0.134%), neg=0, invalid=766 0061: dt=15.552000, rms=0.670 (0.153%), neg=0, invalid=766 0062: dt=15.552000, rms=0.668 (0.275%), neg=0, invalid=766 0063: dt=15.552000, rms=0.665 (0.411%), neg=0, invalid=766 0064: dt=15.552000, rms=0.662 (0.528%), neg=0, invalid=766 0065: dt=15.552000, rms=0.658 (0.610%), neg=0, invalid=766 0066: dt=15.552000, rms=0.654 (0.632%), neg=0, invalid=766 0067: dt=15.552000, rms=0.650 (0.625%), neg=0, invalid=766 0068: dt=15.552000, rms=0.646 (0.614%), neg=0, invalid=766 0069: dt=15.552000, rms=0.642 (0.585%), neg=0, invalid=766 0070: dt=15.552000, rms=0.638 (0.553%), neg=0, invalid=766 0071: dt=15.552000, rms=0.635 (0.524%), neg=0, invalid=766 0072: dt=15.552000, rms=0.632 (0.487%), neg=0, invalid=766 0073: dt=15.552000, rms=0.629 (0.438%), neg=0, invalid=766 0074: dt=15.552000, rms=0.627 (0.376%), neg=0, invalid=766 0075: dt=15.552000, rms=0.625 (0.326%), neg=0, invalid=766 0076: dt=15.552000, rms=0.623 (0.288%), neg=0, invalid=766 0077: dt=15.552000, rms=0.621 (0.277%), neg=0, invalid=766 0078: dt=15.552000, rms=0.619 (0.273%), neg=0, invalid=766 0079: dt=15.552000, rms=0.618 (0.250%), neg=0, invalid=766 0080: dt=15.552000, rms=0.616 (0.216%), neg=0, invalid=766 0081: dt=15.552000, rms=0.615 (0.189%), neg=0, invalid=766 0082: dt=15.552000, rms=0.614 (0.168%), neg=0, invalid=766 0083: dt=15.552000, rms=0.613 (0.155%), neg=0, invalid=766 0084: dt=15.552000, rms=0.612 (0.144%), neg=0, invalid=766 0085: dt=15.552000, rms=0.612 (0.142%), neg=0, invalid=766 0086: dt=15.552000, rms=0.611 (0.137%), neg=0, invalid=766 0087: dt=15.552000, rms=0.610 (0.116%), neg=0, invalid=766 0088: dt=15.552000, rms=0.609 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48699.328 ms 0089: dt=145.152000, rms=0.609 (0.045%), neg=0, invalid=766 0090: dt=145.152000, rms=0.609 (-0.265%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45710.562 ms 0091: dt=36.288000, rms=0.609 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39639.340 ms 0092: dt=25.920000, rms=0.609 (0.022%), neg=0, invalid=766 0093: dt=25.920000, rms=0.609 (-0.008%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42080.406 ms 0094: dt=2.000000, rms=0.638 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41849.926 ms 0095: dt=0.400000, rms=0.638 (0.000%), neg=0, invalid=766 0096: dt=0.400000, rms=0.638 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38981.105 ms 0097: dt=0.000000, rms=0.638 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.724, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38989.539 ms 0098: dt=4.603376, rms=0.705 (2.669%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36581.629 ms 0099: dt=2.196429, rms=0.704 (0.135%), neg=0, invalid=766 0100: dt=2.196429, rms=0.704 (-0.032%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36811.328 ms 0101: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.794, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36698.816 ms 0102: dt=1.156934, rms=0.789 (0.713%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36550.898 ms 0103: dt=1.809524, rms=0.783 (0.757%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36569.535 ms 0104: dt=0.450000, rms=0.782 (0.057%), neg=0, invalid=766 0105: dt=0.450000, rms=0.782 (0.022%), neg=0, invalid=766 0106: dt=0.450000, rms=0.782 (0.007%), neg=0, invalid=766 0107: dt=0.450000, rms=0.782 (-0.075%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.782, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36500.094 ms 0108: dt=1.280000, rms=0.781 (0.176%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34324.285 ms 0109: dt=0.000000, rms=0.781 (0.001%), neg=0, invalid=766 0110: dt=0.100000, rms=0.781 (-0.012%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.717, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36480.422 ms 0111: dt=0.448000, rms=0.694 (3.237%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31648.104 ms 0112: dt=0.000000, rms=0.694 (0.008%), neg=0, invalid=766 0113: dt=0.050000, rms=0.694 (-0.436%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31659.770 ms 0114: dt=0.000000, rms=0.694 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.17736 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (2202 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2202 voxels, peak = 4), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.11250 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (1889 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1889 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.10366 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (324 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (324 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.08467 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, overlap=0.998) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, peak = 97), gca=97.0 gca peak = 0.24007 (63) mri peak = 0.07136 (58) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (547 voxels, overlap=0.930) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (547 voxels, peak = 58), gca=58.3 gca peak = 0.29892 (64) mri peak = 0.07486 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (547 voxels, overlap=0.960) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (547 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.08462 (107) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (56773 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (56773 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.07394 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (59084 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (59084 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03687 (60) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (18709 voxels, overlap=0.711) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (18709 voxels, peak = 57), gca=56.7 gca peak = 0.13270 (63) mri peak = 0.03244 (63) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (19657 voxels, overlap=0.506) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (19657 voxels, peak = 60), gca=59.8 gca peak = 0.15182 (70) mri peak = 0.07620 (64) Right_Caudate (50): linear fit = 0.88 x + 0.0 (325 voxels, overlap=0.006) Right_Caudate (50): linear fit = 0.88 x + 0.0 (325 voxels, peak = 61), gca=61.2 gca peak = 0.14251 (76) mri peak = 0.08822 (70) Left_Caudate (11): linear fit = 0.85 x + 0.0 (790 voxels, overlap=0.325) Left_Caudate (11): linear fit = 0.85 x + 0.0 (790 voxels, peak = 65), gca=64.6 gca peak = 0.12116 (60) mri peak = 0.03814 (57) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (22282 voxels, overlap=0.842) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (22282 voxels, peak = 57), gca=57.0 gca peak = 0.12723 (61) mri peak = 0.04204 (55) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (25897 voxels, overlap=0.843) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (25897 voxels, peak = 58), gca=58.0 gca peak = 0.22684 (88) mri peak = 0.07970 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7062 voxels, overlap=0.581) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7062 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.08025 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6914 voxels, overlap=0.617) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6914 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.11437 (56) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, overlap=0.832) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.12892 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (311 voxels, overlap=0.931) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (311 voxels, peak = 56), gca=55.8 gca peak = 0.10129 (93) mri peak = 0.05147 (90) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4627 voxels, overlap=0.899) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4627 voxels, peak = 91), gca=90.7 gca peak = 0.12071 (89) mri peak = 0.06659 (84) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3304 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3304 voxels, peak = 87), gca=86.8 gca peak = 0.13716 (82) mri peak = 0.05625 (79) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2119 voxels, overlap=0.662) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2119 voxels, peak = 76), gca=75.8 gca peak = 0.15214 (84) mri peak = 0.04259 (83) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2306 voxels, overlap=0.711) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2306 voxels, peak = 80), gca=79.8 gca peak = 0.08983 (85) mri peak = 0.06377 (85) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10520 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10520 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.09287 (101) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (876 voxels, overlap=0.590) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (876 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.10302 (100) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1092 voxels, overlap=0.757) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1092 voxels, peak = 99), gca=98.7 gca peak = 0.21100 (36) mri peak = 0.11115 ( 5) gca peak = 0.13542 (27) mri peak = 0.16850 ( 8) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (409 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (409 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.716, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40376.922 ms 0115: dt=129.472000, rms=0.708 (1.092%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40472.582 ms 0116: dt=295.936000, rms=0.703 (0.772%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40307.926 ms 0117: dt=73.984000, rms=0.701 (0.304%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44099.469 ms 0118: dt=369.920000, rms=0.697 (0.502%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37676.801 ms 0119: dt=32.368000, rms=0.696 (0.123%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39343.223 ms 0120: dt=32.368000, rms=0.696 (0.027%), neg=0, invalid=766 0121: dt=32.368000, rms=0.696 (0.021%), neg=0, invalid=766 0122: dt=32.368000, rms=0.696 (0.036%), neg=0, invalid=766 0123: dt=32.368000, rms=0.695 (0.064%), neg=0, invalid=766 0124: dt=32.368000, rms=0.694 (0.107%), neg=0, invalid=766 0125: dt=32.368000, rms=0.693 (0.139%), neg=0, invalid=766 0126: dt=32.368000, rms=0.692 (0.143%), neg=0, invalid=766 0127: dt=32.368000, rms=0.692 (0.128%), neg=0, invalid=766 0128: dt=32.368000, rms=0.691 (0.116%), neg=0, invalid=766 0129: dt=32.368000, rms=0.690 (0.108%), neg=0, invalid=766 0130: dt=32.368000, rms=0.689 (0.108%), neg=0, invalid=766 0131: dt=32.368000, rms=0.688 (0.124%), neg=0, invalid=766 0132: dt=32.368000, rms=0.688 (0.134%), neg=0, invalid=766 0133: dt=32.368000, rms=0.687 (0.136%), neg=0, invalid=766 0134: dt=32.368000, rms=0.686 (0.120%), neg=0, invalid=766 0135: dt=32.368000, rms=0.685 (0.108%), neg=0, invalid=766 0136: dt=32.368000, rms=0.684 (0.094%), neg=0, invalid=766 0137: dt=32.368000, rms=0.684 (0.085%), neg=0, invalid=766 0138: dt=32.368000, rms=0.683 (0.084%), neg=0, invalid=766 0139: dt=32.368000, rms=0.683 (0.093%), neg=0, invalid=766 0140: dt=32.368000, rms=0.682 (0.101%), neg=0, invalid=766 0141: dt=32.368000, rms=0.681 (0.102%), neg=0, invalid=766 0142: dt=32.368000, rms=0.681 (0.098%), neg=0, invalid=766 0143: dt=32.368000, rms=0.680 (0.087%), neg=0, invalid=766 0144: dt=32.368000, rms=0.679 (0.080%), neg=0, invalid=766 0145: dt=32.368000, rms=0.679 (0.075%), neg=0, invalid=766 0146: dt=32.368000, rms=0.678 (0.077%), neg=0, invalid=766 0147: dt=32.368000, rms=0.678 (0.072%), neg=0, invalid=766 0148: dt=32.368000, rms=0.677 (0.074%), neg=0, invalid=766 0149: dt=32.368000, rms=0.677 (0.075%), neg=0, invalid=766 0150: dt=32.368000, rms=0.676 (0.070%), neg=0, invalid=766 0151: dt=32.368000, rms=0.676 (0.073%), neg=0, invalid=766 0152: dt=32.368000, rms=0.675 (0.068%), neg=0, invalid=766 0153: dt=32.368000, rms=0.675 (0.064%), neg=0, invalid=766 0154: dt=32.368000, rms=0.675 (0.064%), neg=0, invalid=766 0155: dt=32.368000, rms=0.674 (0.065%), neg=0, invalid=766 0156: dt=32.368000, rms=0.674 (0.067%), neg=0, invalid=766 0157: dt=32.368000, rms=0.673 (0.068%), neg=0, invalid=766 0158: dt=32.368000, rms=0.673 (0.064%), neg=0, invalid=766 0159: dt=32.368000, rms=0.672 (0.059%), neg=0, invalid=766 0160: dt=32.368000, rms=0.672 (0.057%), neg=0, invalid=766 0161: dt=32.368000, rms=0.672 (0.052%), neg=0, invalid=766 0162: dt=32.368000, rms=0.671 (0.053%), neg=0, invalid=766 0163: dt=32.368000, rms=0.671 (0.052%), neg=0, invalid=766 0164: dt=32.368000, rms=0.671 (0.052%), neg=0, invalid=766 0165: dt=32.368000, rms=0.670 (0.051%), neg=0, invalid=766 0166: dt=32.368000, rms=0.670 (0.045%), neg=0, invalid=766 0167: dt=32.368000, rms=0.670 (0.058%), neg=0, invalid=766 0168: dt=32.368000, rms=0.669 (0.041%), neg=0, invalid=766 0169: dt=32.368000, rms=0.669 (0.033%), neg=0, invalid=766 0170: dt=32.368000, rms=0.669 (0.035%), neg=0, invalid=766 0171: dt=32.368000, rms=0.668 (0.058%), neg=0, invalid=766 0172: dt=32.368000, rms=0.668 (0.045%), neg=0, invalid=766 0173: dt=32.368000, rms=0.668 (0.037%), neg=0, invalid=766 0174: dt=32.368000, rms=0.668 (0.027%), neg=0, invalid=766 0175: dt=32.368000, rms=0.668 (0.025%), neg=0, invalid=766 0176: dt=32.368000, rms=0.667 (0.047%), neg=0, invalid=766 0177: dt=32.368000, rms=0.667 (0.033%), neg=0, invalid=766 0178: dt=32.368000, rms=0.667 (0.032%), neg=0, invalid=766 0179: dt=32.368000, rms=0.667 (0.028%), neg=0, invalid=766 0180: dt=32.368000, rms=0.666 (0.047%), neg=0, invalid=766 0181: dt=32.368000, rms=0.666 (0.034%), neg=0, invalid=766 0182: dt=32.368000, rms=0.666 (0.029%), neg=0, invalid=766 0183: dt=32.368000, rms=0.666 (0.026%), neg=0, invalid=766 0184: dt=32.368000, rms=0.666 (0.027%), neg=0, invalid=766 0185: dt=32.368000, rms=0.665 (0.039%), neg=0, invalid=766 0186: dt=32.368000, rms=0.665 (0.042%), neg=0, invalid=766 0187: dt=32.368000, rms=0.665 (0.034%), neg=0, invalid=766 0188: dt=32.368000, rms=0.665 (0.026%), neg=0, invalid=766 0189: dt=32.368000, rms=0.664 (0.017%), neg=0, invalid=766 0190: dt=32.368000, rms=0.664 (0.015%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44507.836 ms 0191: dt=517.888000, rms=0.664 (0.069%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41866.668 ms 0192: dt=0.000000, rms=0.664 (-0.003%), neg=0, invalid=766 0193: dt=0.850000, rms=0.664 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40584.688 ms 0194: dt=32.368000, rms=0.664 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42222.238 ms 0195: dt=73.984000, rms=0.664 (0.029%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42389.949 ms 0196: dt=443.904000, rms=0.661 (0.400%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38528.496 ms 0197: dt=18.496000, rms=0.661 (0.014%), neg=0, invalid=766 0198: dt=18.496000, rms=0.661 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.662, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40320.742 ms 0199: dt=62.208000, rms=0.657 (0.714%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40113.469 ms 0200: dt=36.288000, rms=0.650 (1.026%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34931.402 ms 0201: dt=20.736000, rms=0.648 (0.248%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37476.930 ms 0202: dt=145.152000, rms=0.638 (1.633%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34800.609 ms 0203: dt=20.736000, rms=0.636 (0.360%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37653.406 ms 0204: dt=145.152000, rms=0.628 (1.168%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34807.188 ms 0205: dt=20.736000, rms=0.627 (0.254%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40118.078 ms 0206: dt=145.152000, rms=0.621 (0.825%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35492.441 ms 0207: dt=20.736000, rms=0.620 (0.290%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38621.285 ms 0208: dt=124.416000, rms=0.616 (0.550%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32528.756 ms 0209: dt=1.944000, rms=0.616 (0.023%), neg=0, invalid=766 0210: dt=0.015187, rms=0.616 (0.000%), neg=0, invalid=766 0211: dt=0.007594, rms=0.616 (0.000%), neg=0, invalid=766 0212: dt=0.000475, rms=0.616 (0.000%), neg=0, invalid=766 0213: dt=0.000237, rms=0.616 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17615.707 ms 0214: dt=0.000000, rms=0.616 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17389.369 ms 0215: dt=0.000000, rms=0.616 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.620, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18359.658 ms 0216: dt=0.000000, rms=0.620 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.620, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17730.205 ms 0217: dt=0.000000, rms=0.620 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36629.117 ms 0218: dt=1.008000, rms=0.628 (0.868%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35526.543 ms 0219: dt=1.008000, rms=0.623 (0.813%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36530.410 ms 0220: dt=1.008000, rms=0.618 (0.757%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38460.578 ms 0221: dt=3.456000, rms=0.603 (2.366%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42353.246 ms 0222: dt=4.032000, rms=0.590 (2.144%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39953.812 ms 0223: dt=4.032000, rms=0.581 (1.601%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36862.754 ms 0224: dt=4.032000, rms=0.574 (1.224%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37022.039 ms 0225: dt=4.032000, rms=0.568 (0.943%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37395.637 ms 0226: dt=13.824000, rms=0.554 (2.464%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36885.152 ms 0227: dt=3.456000, rms=0.553 (0.219%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34372.289 ms 0228: dt=4.032000, rms=0.552 (0.248%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36925.977 ms 0229: dt=2.880000, rms=0.551 (0.148%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36874.781 ms 0230: dt=11.520000, rms=0.548 (0.537%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36652.754 ms 0231: dt=2.880000, rms=0.547 (0.127%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34880.195 ms 0232: dt=4.032000, rms=0.547 (0.136%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35295.684 ms 0233: dt=4.032000, rms=0.546 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37560.172 ms 0234: dt=13.824000, rms=0.544 (0.300%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37638.668 ms 0235: dt=2.880000, rms=0.544 (0.109%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38039.496 ms 0236: dt=11.520000, rms=0.543 (0.225%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39090.027 ms 0237: dt=3.000000, rms=0.542 (0.041%), neg=0, invalid=766 0238: dt=3.000000, rms=0.542 (0.064%), neg=0, invalid=766 0239: dt=3.000000, rms=0.542 (0.072%), neg=0, invalid=766 0240: dt=3.000000, rms=0.541 (0.114%), neg=0, invalid=766 0241: dt=3.000000, rms=0.540 (0.131%), neg=0, invalid=766 0242: dt=3.000000, rms=0.539 (0.162%), neg=0, invalid=766 0243: dt=3.000000, rms=0.539 (0.154%), neg=0, invalid=766 0244: dt=3.000000, rms=0.538 (0.154%), neg=0, invalid=766 0245: dt=3.000000, rms=0.537 (0.142%), neg=0, invalid=766 0246: dt=3.000000, rms=0.537 (0.015%), neg=0, invalid=766 0247: dt=3.000000, rms=0.537 (0.025%), neg=0, invalid=766 0248: dt=3.000000, rms=0.537 (0.024%), neg=0, invalid=766 0249: dt=3.000000, rms=0.537 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38703.980 ms 0250: dt=16.128000, rms=0.536 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38042.906 ms 0251: dt=2.304000, rms=0.536 (0.015%), neg=0, invalid=766 0252: dt=2.304000, rms=0.536 (0.015%), neg=0, invalid=766 0253: dt=2.304000, rms=0.536 (0.013%), neg=0, invalid=766 0254: dt=2.304000, rms=0.536 (0.022%), neg=0, invalid=766 0255: dt=2.304000, rms=0.536 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34753.508 ms 0256: dt=2.304000, rms=0.536 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.536, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38737.656 ms 0257: dt=0.000000, rms=0.536 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.561, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34894.863 ms 0258: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32575.875 ms 0259: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.518, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36183.488 ms 0260: dt=0.080000, rms=0.515 (0.613%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34982.977 ms 0261: dt=0.028000, rms=0.514 (0.184%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35122.094 ms 0262: dt=0.147584, rms=0.510 (0.901%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31695.402 ms 0263: dt=0.020000, rms=0.509 (0.089%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31681.566 ms 0264: dt=0.028000, rms=0.508 (0.123%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34207.219 ms 0265: dt=0.080000, rms=0.507 (0.333%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32000.645 ms 0266: dt=0.028000, rms=0.506 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33348.996 ms 0267: dt=0.028000, rms=0.506 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32181.971 ms 0268: dt=0.028000, rms=0.505 (0.092%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32169.168 ms 0269: dt=0.028000, rms=0.505 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32189.926 ms 0270: dt=0.028000, rms=0.504 (0.084%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32177.215 ms 0271: dt=0.028000, rms=0.504 (0.080%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32316.562 ms 0272: dt=0.028000, rms=0.504 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32166.346 ms 0273: dt=0.028000, rms=0.503 (0.074%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32165.814 ms 0274: dt=0.028000, rms=0.503 (0.069%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32471.240 ms 0275: dt=0.028000, rms=0.503 (0.071%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32174.217 ms 0276: dt=0.028000, rms=0.502 (0.062%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32180.057 ms 0277: dt=0.028000, rms=0.502 (0.060%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32172.637 ms 0278: dt=0.028000, rms=0.502 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32167.246 ms 0279: dt=0.028000, rms=0.501 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32172.689 ms 0280: dt=0.028000, rms=0.501 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32167.576 ms 0281: dt=0.028000, rms=0.501 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34667.246 ms 0282: dt=0.112000, rms=0.500 (0.207%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34619.449 ms 0283: dt=0.096916, rms=0.499 (0.152%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32392.215 ms 0284: dt=0.028000, rms=0.499 (0.037%), neg=0, invalid=766 0285: dt=0.028000, rms=0.499 (0.037%), neg=0, invalid=766 0286: dt=0.028000, rms=0.498 (0.069%), neg=0, invalid=766 0287: dt=0.028000, rms=0.498 (0.092%), neg=0, invalid=766 0288: dt=0.028000, rms=0.497 (0.115%), neg=0, invalid=766 0289: dt=0.028000, rms=0.497 (0.132%), neg=0, invalid=766 0290: dt=0.028000, rms=0.496 (0.143%), neg=0, invalid=766 0291: dt=0.028000, rms=0.495 (0.141%), neg=0, invalid=766 0292: dt=0.028000, rms=0.495 (0.139%), neg=0, invalid=766 0293: dt=0.028000, rms=0.494 (0.130%), neg=0, invalid=766 0294: dt=0.028000, rms=0.493 (0.130%), neg=0, invalid=766 0295: dt=0.028000, rms=0.493 (0.120%), neg=0, invalid=766 0296: dt=0.028000, rms=0.492 (0.110%), neg=0, invalid=766 0297: dt=0.028000, rms=0.492 (0.094%), neg=0, invalid=766 0298: dt=0.028000, rms=0.492 (-0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32474.764 ms 0299: dt=0.000000, rms=0.492 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34892.195 ms 0300: dt=0.112000, rms=0.490 (0.234%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34869.137 ms 0301: dt=0.112000, rms=0.490 (0.176%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32469.297 ms 0302: dt=0.028000, rms=0.489 (0.034%), neg=0, invalid=766 0303: dt=0.014000, rms=0.489 (0.016%), neg=0, invalid=766 0304: dt=0.014000, rms=0.489 (0.017%), neg=0, invalid=766 0305: dt=0.014000, rms=0.489 (0.030%), neg=0, invalid=766 0306: dt=0.014000, rms=0.489 (0.039%), neg=0, invalid=766 0307: dt=0.014000, rms=0.489 (0.048%), neg=0, invalid=766 0308: dt=0.014000, rms=0.488 (0.056%), neg=0, invalid=766 0309: dt=0.014000, rms=0.488 (0.057%), neg=0, invalid=766 0310: dt=0.014000, rms=0.488 (0.060%), neg=0, invalid=766 0311: dt=0.014000, rms=0.488 (0.063%), neg=0, invalid=766 0312: dt=0.014000, rms=0.488 (0.005%), neg=0, invalid=766 0313: dt=0.014000, rms=0.488 (0.009%), neg=0, invalid=766 0314: dt=0.014000, rms=0.487 (0.017%), neg=0, invalid=766 0315: dt=0.014000, rms=0.487 (0.018%), neg=0, invalid=766 0316: dt=0.014000, rms=0.487 (0.019%), neg=0, invalid=766 0317: dt=0.014000, rms=0.487 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35181.227 ms 0318: dt=0.112000, rms=0.487 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32524.121 ms 0319: dt=0.028000, rms=0.487 (0.007%), neg=0, invalid=766 0320: dt=0.007000, rms=0.487 (0.001%), neg=0, invalid=766 0321: dt=0.007000, rms=0.487 (0.002%), neg=0, invalid=766 0322: dt=0.007000, rms=0.487 (0.004%), neg=0, invalid=766 0323: dt=0.007000, rms=0.487 (0.002%), neg=0, invalid=766 0324: dt=0.007000, rms=0.487 (0.006%), neg=0, invalid=766 0325: dt=0.007000, rms=0.487 (0.007%), neg=0, invalid=766 0326: dt=0.007000, rms=0.487 (0.007%), neg=0, invalid=766 0327: dt=0.007000, rms=0.487 (0.008%), neg=0, invalid=766 0328: dt=0.007000, rms=0.487 (0.008%), neg=0, invalid=766 0329: dt=0.007000, rms=0.487 (0.005%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.485, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42040.293 ms iter 0, gcam->neg = 120 after 45 iterations, nbhd size=4, neg = 0 0330: dt=44.800000, rms=0.474 (2.196%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41806.191 ms iter 0, gcam->neg = 22 after 18 iterations, nbhd size=2, neg = 0 0331: dt=11.200000, rms=0.473 (0.199%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 22 iterations, nbhd size=3, neg = 0 0332: dt=11.200000, rms=0.472 (0.216%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 29 iterations, nbhd size=4, neg = 0 0333: dt=11.200000, rms=0.471 (0.334%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 55 iterations, nbhd size=3, neg = 0 0334: dt=11.200000, rms=0.469 (0.353%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24574.654 ms iter 1, dt=0.000875: new neg 1, old_neg 1, delta 0, rms=0.003 (21.684%) gcamFindOptimalTimeStep: Complete in 24559.633 ms iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (5.487%) 0335: dt=11.200000, rms=0.468 (0.281%), neg=0, invalid=766 0336: dt=11.200000, rms=0.467 (0.176%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0337: dt=11.200000, rms=0.466 (0.218%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 25 iterations, nbhd size=3, neg = 0 0338: dt=11.200000, rms=0.465 (0.156%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 30 iterations, nbhd size=4, neg = 0 0339: dt=11.200000, rms=0.465 (0.120%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0340: dt=11.200000, rms=0.464 (0.094%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44585.613 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0341: dt=11.200000, rms=0.464 (0.073%), neg=0, invalid=766 0342: dt=11.200000, rms=0.463 (0.076%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 20 iterations, nbhd size=3, neg = 0 0343: dt=11.200000, rms=0.463 (0.116%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 14 iterations, nbhd size=2, neg = 0 0344: dt=11.200000, rms=0.462 (0.120%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 22 iterations, nbhd size=3, neg = 0 0345: dt=11.200000, rms=0.462 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 21 iterations, nbhd size=2, neg = 0 0346: dt=11.200000, rms=0.462 (0.106%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0347: dt=11.200000, rms=0.461 (0.077%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42950.047 ms iter 0, gcam->neg = 6 after 25 iterations, nbhd size=3, neg = 0 0348: dt=44.800000, rms=0.457 (0.858%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46813.598 ms iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0349: dt=9.176471, rms=0.456 (0.208%), neg=0, invalid=766 0350: dt=9.176471, rms=0.456 (0.108%), neg=0, invalid=766 0351: dt=9.176471, rms=0.455 (0.108%), neg=0, invalid=766 0352: dt=9.176471, rms=0.455 (0.152%), neg=0, invalid=766 0353: dt=9.176471, rms=0.454 (0.108%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0354: dt=9.176471, rms=0.453 (0.160%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 14 iterations, nbhd size=2, neg = 0 0355: dt=9.176471, rms=0.453 (0.091%), neg=0, invalid=766 0356: dt=9.176471, rms=0.453 (0.099%), neg=0, invalid=766 0357: dt=9.176471, rms=0.452 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43592.645 ms 0358: dt=9.600000, rms=0.452 (0.052%), neg=0, invalid=766 0359: dt=9.600000, rms=0.452 (0.009%), neg=0, invalid=766 0360: dt=9.600000, rms=0.452 (0.045%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0361: dt=9.600000, rms=0.451 (0.042%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0362: dt=9.600000, rms=0.451 (0.034%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48349.059 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0363: dt=2.880000, rms=0.455 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47411.305 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0364: dt=2.880000, rms=0.455 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 11 iterations, nbhd size=1, neg = 0 0365: dt=2.880000, rms=0.455 (-0.025%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45540.355 ms iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0366: dt=1.793103, rms=0.455 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52148.574 ms iter 0, gcam->neg = 1 after 53 iterations, nbhd size=1, neg = 0 0367: dt=4.727273, rms=0.455 (0.041%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44482.699 ms iter 0, gcam->neg = 11 after 33 iterations, nbhd size=4, neg = 0 0368: dt=4.032000, rms=0.455 (0.042%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44377.934 ms iter 0, gcam->neg = 18 after 30 iterations, nbhd size=3, neg = 0 0369: dt=3.456000, rms=0.455 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41391.777 ms iter 0, gcam->neg = 12 after 29 iterations, nbhd size=3, neg = 0 0370: dt=4.032000, rms=0.454 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42202.617 ms iter 0, gcam->neg = 12 after 26 iterations, nbhd size=3, neg = 0 0371: dt=4.032000, rms=0.454 (0.074%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41588.262 ms iter 0, gcam->neg = 31 after 31 iterations, nbhd size=3, neg = 0 0372: dt=9.216000, rms=0.454 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45274.469 ms 0373: dt=1.008000, rms=0.454 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0374: dt=1.008000, rms=0.454 (0.019%), neg=0, invalid=766 0375: dt=1.008000, rms=0.453 (0.042%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0376: dt=1.008000, rms=0.453 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0377: dt=1.008000, rms=0.453 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0378: dt=1.008000, rms=0.453 (0.054%), neg=0, invalid=766 0379: dt=1.008000, rms=0.452 (0.056%), neg=0, invalid=766 0380: dt=1.008000, rms=0.452 (0.051%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.457, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42025.172 ms 0381: dt=0.000000, rms=0.457 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42033.863 ms 0382: dt=0.000000, rms=0.457 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44417.324 ms iter 0, gcam->neg = 801 after 22 iterations, nbhd size=2, neg = 0 0383: dt=1.388552, rms=0.420 (6.578%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44422.270 ms 0384: dt=0.000250, rms=0.420 (-0.001%), neg=0, invalid=766 0385: dt=0.000250, rms=0.420 (0.001%), neg=0, invalid=766 0386: dt=0.000250, rms=0.420 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44420.059 ms 0387: dt=0.000094, rms=0.420 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41979.285 ms 0388: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44407.059 ms iter 0, gcam->neg = 169 after 16 iterations, nbhd size=2, neg = 0 0389: dt=0.220896, rms=0.407 (1.109%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45431.391 ms 0390: dt=0.001750, rms=0.407 (-0.013%), neg=0, invalid=766 0391: dt=0.001750, rms=0.407 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0392: dt=0.001750, rms=0.407 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0393: dt=0.001750, rms=0.407 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0394: dt=0.001750, rms=0.407 (0.016%), neg=0, invalid=766 0395: dt=0.001750, rms=0.407 (0.019%), neg=0, invalid=766 0396: dt=0.001750, rms=0.407 (0.021%), neg=0, invalid=766 0397: dt=0.001750, rms=0.407 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0398: dt=0.001750, rms=0.407 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0399: dt=0.001750, rms=0.406 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0400: dt=0.001750, rms=0.406 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0401: dt=0.001750, rms=0.406 (0.029%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44432.422 ms iter 0, gcam->neg = 163 after 21 iterations, nbhd size=2, neg = 0 0402: dt=0.256000, rms=0.402 (1.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44423.914 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0403: dt=0.001500, rms=0.402 (-0.010%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0404: dt=0.001500, rms=0.402 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0405: dt=0.001500, rms=0.402 (-0.006%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.402, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44377.184 ms iter 0, gcam->neg = 57 after 7 iterations, nbhd size=1, neg = 0 0406: dt=0.064000, rms=0.400 (0.318%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53666.801 ms 0407: dt=0.000060, rms=0.400 (-0.010%), neg=0, invalid=766 0408: dt=0.000060, rms=0.400 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0409: dt=0.000060, rms=0.400 (0.001%), neg=0, invalid=766 0410: dt=0.000060, rms=0.400 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0411: dt=0.000060, rms=0.400 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43938.473 ms iter 0, gcam->neg = 91 after 19 iterations, nbhd size=2, neg = 0 0412: dt=0.080000, rms=0.399 (0.469%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43758.387 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0413: dt=0.001000, rms=0.399 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0414: dt=0.001000, rms=0.398 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0415: dt=0.001000, rms=0.398 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0416: dt=0.001000, rms=0.398 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0417: dt=0.001000, rms=0.398 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0418: dt=0.001000, rms=0.398 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0419: dt=0.001000, rms=0.398 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0420: dt=0.001000, rms=0.398 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0421: dt=0.001000, rms=0.398 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0422: dt=0.001000, rms=0.398 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0423: dt=0.001000, rms=0.398 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0424: dt=0.001000, rms=0.398 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=0.001000, rms=0.397 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0426: dt=0.001000, rms=0.397 (0.035%), neg=0, invalid=766 0427: dt=0.001000, rms=0.397 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0428: dt=0.001000, rms=0.397 (0.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43950.898 ms iter 0, gcam->neg = 66 after 18 iterations, nbhd size=2, neg = 0 0429: dt=0.079878, rms=0.396 (0.302%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43527.016 ms 0430: dt=0.000438, rms=0.396 (0.004%), neg=0, invalid=766 0431: dt=0.000438, rms=0.396 (0.002%), neg=0, invalid=766 0432: dt=0.000438, rms=0.396 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0433: dt=0.000438, rms=0.396 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0434: dt=0.000438, rms=0.396 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0435: dt=0.000438, rms=0.396 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0436: dt=0.000438, rms=0.396 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0437: dt=0.000438, rms=0.396 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0438: dt=0.000438, rms=0.396 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0439: dt=0.000438, rms=0.396 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43560.879 ms iter 0, gcam->neg = 49 after 16 iterations, nbhd size=2, neg = 0 0440: dt=0.064000, rms=0.395 (0.204%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43527.664 ms iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0441: dt=0.001500, rms=0.395 (-0.008%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42754.367 ms iter 0, gcam->neg = 18 after 21 iterations, nbhd size=2, neg = 0 0442: dt=1.600000, rms=0.396 (-0.222%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40410.887 ms iter 0, gcam->neg = 57 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.010, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23112.650 ms iter 1, dt=0.000000: new neg 4, old_neg 4, delta 0, rms=0.010 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0443: dt=8.000000, rms=0.396 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.396, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42747.469 ms iter 0, gcam->neg = 54 after 34 iterations, nbhd size=3, neg = 0 0444: dt=0.700000, rms=0.395 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44310.402 ms iter 0, gcam->neg = 41 after 38 iterations, nbhd size=4, neg = 0 0445: dt=0.432000, rms=0.395 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23105.676 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0446: dt=0.432000, rms=0.395 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42747.656 ms iter 0, gcam->neg = 67 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23100.592 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0447: dt=1.269231, rms=0.395 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42767.422 ms iter 0, gcam->neg = 18 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23575.539 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0448: dt=0.079487, rms=0.395 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43239.023 ms iter 0, gcam->neg = 24 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23080.486 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0449: dt=0.112000, rms=0.395 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42716.129 ms 0450: dt=0.000109, rms=0.395 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42755.102 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0451: dt=0.001000, rms=0.395 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42748.219 ms 0452: dt=0.001750, rms=0.395 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42901.301 ms 0453: dt=0.001750, rms=0.395 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 15 iterations, nbhd size=2, neg = 0 0454: dt=0.001750, rms=0.395 (0.008%), neg=0, invalid=766 0455: dt=0.001750, rms=0.395 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 17 iterations, nbhd size=2, neg = 0 0456: dt=0.001750, rms=0.395 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0457: dt=0.001750, rms=0.395 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0458: dt=0.001750, rms=0.394 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0459: dt=0.001750, rms=0.394 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 34 iterations, nbhd size=4, neg = 0 0460: dt=0.001750, rms=0.394 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 53 iterations, nbhd size=4, neg = 0 0461: dt=0.001750, rms=0.394 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 27 iterations, nbhd size=4, neg = 0 0462: dt=0.001750, rms=0.394 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0463: dt=0.001750, rms=0.394 (0.050%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 30 iterations, nbhd size=4, neg = 0 0464: dt=0.001750, rms=0.393 (0.048%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23148.309 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0465: dt=0.001750, rms=0.393 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42941.754 ms 0466: dt=0.000438, rms=0.393 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43383.223 ms 0467: dt=0.000438, rms=0.393 (0.003%), neg=0, invalid=766 0468: dt=0.000438, rms=0.393 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0469: dt=0.000438, rms=0.393 (0.005%), neg=0, invalid=766 0470: dt=0.000438, rms=0.393 (0.007%), neg=0, invalid=766 0471: dt=0.000438, rms=0.393 (0.009%), neg=0, invalid=766 0472: dt=0.000438, rms=0.393 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23336.242 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0473: dt=0.000438, rms=0.393 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.393, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43115.191 ms iter 0, gcam->neg = 7 after 26 iterations, nbhd size=3, neg = 0 0474: dt=0.005000, rms=0.393 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43331.176 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0475: dt=0.005000, rms=0.393 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0476: dt=0.005000, rms=0.393 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0477: dt=0.005000, rms=0.393 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 40 iterations, nbhd size=2, neg = 0 0478: dt=0.005000, rms=0.393 (0.059%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 55 iterations, nbhd size=1, neg = 0 0479: dt=0.005000, rms=0.392 (0.073%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 17 iterations, nbhd size=2, neg = 0 0480: dt=0.005000, rms=0.392 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 29 after 41 iterations, nbhd size=1, neg = 0 0481: dt=0.005000, rms=0.392 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23252.076 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0482: dt=0.005000, rms=0.392 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43355.840 ms 0483: dt=0.000438, rms=0.392 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43142.148 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23077.729 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0484: dt=0.001750, rms=0.392 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42859.297 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0485: dt=0.001500, rms=0.391 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42999.270 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0486: dt=0.004999, rms=0.391 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42987.191 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0487: dt=0.003000, rms=0.391 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0488: dt=0.003000, rms=0.391 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0489: dt=0.003000, rms=0.391 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 18 iterations, nbhd size=2, neg = 0 0490: dt=0.003000, rms=0.391 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0491: dt=0.003000, rms=0.391 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0492: dt=0.003000, rms=0.391 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 15 iterations, nbhd size=2, neg = 0 0493: dt=0.003000, rms=0.390 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 26 iterations, nbhd size=3, neg = 0 0494: dt=0.003000, rms=0.390 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 16 iterations, nbhd size=2, neg = 0 0495: dt=0.003000, rms=0.390 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 15 iterations, nbhd size=2, neg = 0 0496: dt=0.003000, rms=0.390 (0.075%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 7 iterations, nbhd size=1, neg = 0 0497: dt=0.003000, rms=0.389 (0.078%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 28 iterations, nbhd size=3, neg = 0 0498: dt=0.003000, rms=0.389 (0.074%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 33 iterations, nbhd size=4, neg = 0 0499: dt=0.003000, rms=0.389 (0.071%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43149.039 ms iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0500: dt=0.003000, rms=0.389 (0.015%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43507.664 ms iter 0, gcam->neg = 2 after 18 iterations, nbhd size=2, neg = 0 0501: dt=0.005000, rms=0.389 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43532.246 ms 0502: dt=0.000438, rms=0.389 (0.002%), neg=0, invalid=766 0503: dt=0.000438, rms=0.389 (0.002%), neg=0, invalid=766 0504: dt=0.000438, rms=0.389 (0.004%), neg=0, invalid=766 0505: dt=0.000438, rms=0.388 (0.006%), neg=0, invalid=766 0506: dt=0.000438, rms=0.388 (0.007%), neg=0, invalid=766 0507: dt=0.000438, rms=0.388 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0508: dt=0.000438, rms=0.388 (0.010%), neg=0, invalid=766 0509: dt=0.000438, rms=0.388 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0510: dt=0.000438, rms=0.388 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0511: dt=0.000438, rms=0.388 (0.013%), neg=0, invalid=766 0512: dt=0.000438, rms=0.388 (0.014%), neg=0, invalid=766 0513: dt=0.000438, rms=0.388 (0.014%), neg=0, invalid=766 0514: dt=0.000438, rms=0.388 (0.015%), neg=0, invalid=766 0515: dt=0.000438, rms=0.388 (0.015%), neg=0, invalid=766 0516: dt=0.000438, rms=0.388 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0517: dt=0.000438, rms=0.388 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0518: dt=0.000438, rms=0.388 (0.016%), neg=0, invalid=766 0519: dt=0.000438, rms=0.388 (0.017%), neg=0, invalid=766 0520: dt=0.000438, rms=0.388 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 20 iterations, nbhd size=3, neg = 0 0521: dt=0.000438, rms=0.388 (0.015%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 5 hours, 5 minutes and 53 seconds. #-------------------------------------- #@# CA Reg Inv Sat May 21 15:58:57 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Sat May 21 16:00:08 EDT 2011 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11507877 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 20 seconds. #-------------------------------------- #@# SkullLTA Sat May 21 16:01:29 EDT 2011 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (50, 30, 18) --> (206, 200, 226) using (102, 87, 122) as brain centroid... mean wm in atlas = 126, using box (83,66,96) --> (121, 107,147) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10291.2, old_max_log_p =-10350.7 (thresh=-10340.4) 1.144 -0.032 -0.011 -16.131; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10291.2, old_max_log_p =-10291.2 (thresh=-10280.9) 1.144 -0.032 -0.011 -16.131; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10278.4, old_max_log_p =-10291.2 (thresh=-10280.9) 1.081 0.014 -0.005 -13.982; -0.015 1.253 0.093 -28.629; 0.011 -0.090 0.977 -1.074; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10274.8, old_max_log_p =-10278.4 (thresh=-10268.1) 1.100 -0.026 -0.039 -7.848; 0.020 1.232 0.058 -24.718; 0.047 -0.049 0.997 -10.737; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10268.6, old_max_log_p =-10274.8 (thresh=-10264.5) 1.096 -0.026 -0.031 -7.864; 0.020 1.230 0.058 -24.547; 0.038 -0.049 0.998 -9.788; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10268.6 tol 0.000010 Resulting transform: 1.096 -0.026 -0.031 -7.864; 0.020 1.230 0.058 -24.547; 0.038 -0.049 0.998 -9.788; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10268.6 (old=-10350.7) transform before final EM align: 1.096 -0.026 -0.031 -7.864; 0.020 1.230 0.058 -24.547; 0.038 -0.049 0.998 -9.788; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09640 -0.02582 -0.03112 -7.86352; 0.01966 1.23032 0.05821 -24.54732; 0.03794 -0.04884 0.99825 -9.78758; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1144172.1 after pass:transform: ( 1.10, -0.02, -0.03, -7.86) ( 0.02, 1.23, 0.06, -24.55) ( 0.04, -0.05, 1.00, -9.79) dfp_em_step_func: 008: -log(p) = 1144170.8 after pass:transform: ( 1.10, -0.02, -0.03, -7.86) ( 0.02, 1.23, 0.06, -24.55) ( 0.04, -0.05, 1.00, -9.79) dfp_em_step_func: 009: -log(p) = 1144169.5 after pass:transform: ( 1.10, -0.02, -0.03, -7.86) ( 0.02, 1.23, 0.06, -24.55) ( 0.04, -0.05, 1.00, -9.79) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 1144169.5 tol 0.000000 final transform: 1.099 -0.023 -0.028 -7.864; 0.019 1.231 0.058 -24.547; 0.038 -0.049 0.999 -9.788; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 21 minutes and 1 seconds. #-------------------------------------- #@# SubCort Seg Sat May 21 16:22:30 EDT 2011 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname compute-0-1.local machine x86_64 user khoa Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /space/freesurfer/centos4.0_x86_64/stable5/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.15869 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (6218 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (6218 voxels, peak = 5), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.16733 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (7522 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (7522 voxels, peak = 5), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.10249 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, peak = 97), gca=97.0 gca peak = 0.18160 (96) mri peak = 0.07337 (100) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (368 voxels, overlap=0.848) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (368 voxels, peak = 98), gca=98.4 gca peak = 0.27536 (62) mri peak = 0.07384 (55) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (1358 voxels, overlap=0.612) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (1358 voxels, peak = 54), gca=54.2 gca peak = 0.32745 (63) mri peak = 0.08043 (61) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (1162 voxels, overlap=0.587) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (1162 voxels, peak = 55), gca=55.1 gca peak = 0.08597 (105) mri peak = 0.09287 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (29993 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (29993 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.07768 (109) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (32239 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (32239 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.03490 (60) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (22324 voxels, overlap=0.857) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (22324 voxels, peak = 60), gca=59.8 gca peak = 0.08598 (64) mri peak = 0.03418 (63) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (23531 voxels, overlap=0.796) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (23531 voxels, peak = 61), gca=60.8 gca peak = 0.24164 (71) mri peak = 0.10375 (72) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1151 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1151 voxels, peak = 69), gca=69.2 gca peak = 0.18227 (75) mri peak = 0.06955 (65) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1383 voxels, overlap=0.433) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1383 voxels, peak = 64), gca=63.8 gca peak = 0.10629 (62) mri peak = 0.05084 (57) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (19715 voxels, overlap=0.971) Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (19715 voxels, peak = 59), gca=58.9 gca peak = 0.11668 (59) mri peak = 0.05214 (56) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21566 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21566 voxels, peak = 56), gca=56.0 gca peak = 0.17849 (88) mri peak = 0.12242 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4377 voxels, overlap=0.720) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4377 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.11705 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4362 voxels, overlap=0.723) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4362 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.10400 (56) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (510 voxels, overlap=0.583) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (510 voxels, peak = 59), gca=59.2 gca peak = 0.42394 (62) mri peak = 0.09850 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (612 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (612 voxels, peak = 56), gca=55.8 gca peak = 0.10041 (96) mri peak = 0.06122 (90) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3926 voxels, overlap=0.813) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3926 voxels, peak = 91), gca=91.2 gca peak = 0.13978 (88) mri peak = 0.05915 (88) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3694 voxels, overlap=0.984) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3694 voxels, peak = 86), gca=85.8 gca peak = 0.08514 (81) mri peak = 0.05375 (72) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2182 voxels, overlap=0.603) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2182 voxels, peak = 73), gca=72.9 gca peak = 0.09624 (82) mri peak = 0.05994 (71) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2166 voxels, overlap=0.606) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2166 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.06170 (85) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9781 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9781 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.09032 (101) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1012 voxels, overlap=0.698) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1012 voxels, peak = 100), gca=99.7 gca peak = 0.17004 (92) mri peak = 0.10575 (100) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1081 voxels, overlap=0.857) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1081 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.13369 ( 6) Third_Ventricle (14): linear fit = 0.32 x + 0.0 (186 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.32 x + 0.0 (186 voxels, peak = 12), gca=11.7 gca peak = 0.26069 (23) mri peak = 0.22477 ( 8) Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (473 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (473 voxels, peak = 7), gca=6.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.15869 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6218 voxels, overlap=0.777) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6218 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.16733 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.65 x + 0.0 (7522 voxels, overlap=0.825) Right_Lateral_Ventricle (43): linear fit = 0.65 x + 0.0 (7522 voxels, peak = 6), gca=5.8 gca peak = 0.26236 (97) mri peak = 0.10249 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (363 voxels, peak = 97), gca=97.0 gca peak = 0.16124 (98) mri peak = 0.07337 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (368 voxels, overlap=0.831) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (368 voxels, peak = 98), gca=98.0 gca peak = 0.30443 (54) mri peak = 0.07384 (55) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1358 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1358 voxels, peak = 54), gca=54.0 gca peak = 0.33044 (55) mri peak = 0.08043 (61) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1162 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1162 voxels, peak = 60), gca=60.5 gca peak = 0.08347 (108) mri peak = 0.09287 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29993 voxels, overlap=0.795) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29993 voxels, peak = 108), gca=108.0 gca peak = 0.08790 (111) mri peak = 0.07768 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32239 voxels, overlap=0.753) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32239 voxels, peak = 111), gca=111.0 gca peak = 0.08255 (60) mri peak = 0.03490 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22324 voxels, overlap=0.979) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22324 voxels, peak = 62), gca=61.5 gca peak = 0.09370 (61) mri peak = 0.03418 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23531 voxels, overlap=0.850) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23531 voxels, peak = 63), gca=62.5 gca peak = 0.26772 (69) mri peak = 0.10375 (72) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1151 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1151 voxels, peak = 67), gca=67.3 gca peak = 0.17680 (64) mri peak = 0.06955 (65) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1383 voxels, overlap=0.995) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1383 voxels, peak = 64), gca=64.0 gca peak = 0.11076 (58) mri peak = 0.05084 (57) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19715 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19715 voxels, peak = 59), gca=59.4 gca peak = 0.12352 (57) mri peak = 0.05214 (56) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (21566 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (21566 voxels, peak = 58), gca=58.4 gca peak = 0.16852 (92) mri peak = 0.12242 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4377 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4377 voxels, peak = 92), gca=92.0 gca peak = 0.15715 (93) mri peak = 0.11705 (93) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4362 voxels, overlap=0.995) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (4362 voxels, peak = 91), gca=90.7 gca peak = 0.41355 (59) mri peak = 0.10400 (56) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (510 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (510 voxels, peak = 59), gca=59.0 gca peak = 0.53825 (56) mri peak = 0.09850 (57) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (612 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (612 voxels, peak = 56), gca=56.0 gca peak = 0.10151 (91) mri peak = 0.06122 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3926 voxels, overlap=0.994) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3926 voxels, peak = 91), gca=91.0 gca peak = 0.11274 (83) mri peak = 0.05915 (88) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3694 voxels, overlap=0.998) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3694 voxels, peak = 85), gca=85.1 gca peak = 0.09324 (74) mri peak = 0.05375 (72) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2182 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2182 voxels, peak = 74), gca=74.0 gca peak = 0.11772 (70) mri peak = 0.05994 (71) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2166 voxels, overlap=0.989) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2166 voxels, peak = 70), gca=70.0 gca peak = 0.07366 (90) mri peak = 0.06170 (85) Brain_Stem (16): linear fit = 0.98 x + 0.0 (9781 voxels, overlap=0.855) Brain_Stem (16): linear fit = 0.98 x + 0.0 (9781 voxels, peak = 88), gca=87.8 gca peak = 0.10381 (99) mri peak = 0.09032 (101) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1012 voxels, overlap=0.799) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1012 voxels, peak = 101), gca=101.5 gca peak = 0.13627 (99) mri peak = 0.10575 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1081 voxels, overlap=0.881) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1081 voxels, peak = 99), gca=99.0 gca peak = 0.35640 (14) mri peak = 0.13369 ( 6) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (186 voxels, overlap=0.658) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (186 voxels, peak = 11), gca=10.8 gca peak = 0.33827 ( 9) mri peak = 0.22477 ( 8) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (473 voxels, overlap=0.623) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (473 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.27467 (31) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.53035 (60) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.43631 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.33086 (28) gca peak Right_Accumbens_area = 0.32731 (70) gca peak Right_vessel = 0.77757 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.13994 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.66 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 13893 gm and wm labels changed (%16 to gray, %84 to white out of all changed labels) 329 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 81997 changed. image ll: -2.189, PF=1.000 pass 2: 13483 changed. image ll: -2.187, PF=1.000 pass 3: 5200 changed. pass 4: 2338 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 20 minutes and 19 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/cc_up.lta good_output will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/transforms/cc_up.lta reading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/norm.mgz 6188 voxels in left wm, 15737 in right wm, xrange [125, 130] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 global minimum found at slice 127.0, rotations (-0.31, 0.47) final transformation (x=127.0, yr=-0.310, zr=0.474): 1.000 -0.008 -0.005 2.389; 0.008 1.000 -0.000 28.959; 0.005 0.000 1.000 21.315; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 144 176 eigenvectors: 0.000 -0.008 1.000; -0.002 -1.000 -0.008; 1.000 -0.002 -0.000; writing aseg with callosum to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Sat May 21 16:43:33 EDT 2011 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat May 21 16:43:34 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 2434 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 3 minutes and 38 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 109 gm peak at 61 (61), valley at 35 (35) csf peak at 10, setting threshold to 44 white matter peak found at 111 white matter peak found at 110 gm peak at 61 (61), valley at 36 (36) csf peak at 10, setting threshold to 44 #-------------------------------------------- #@# Mask BFS Sat May 21 16:47:15 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1518505 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat May 21 16:47:19 EDT 2011 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-1.local machine x86_64 user khoa input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-1.local machine x86_64 user khoa input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.2 +- 5.0 [80.0 --> 125.0] GM (70.0) : 68.1 +- 10.3 [30.0 --> 96.0] setting bottom of white matter range to 78.4 setting top of gray matter range to 88.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 3662 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5855 filled 3024 bright non-wm voxels segmented. 2299 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.54 minutes reading wm segmentation from wm.seg.mgz... 260 voxels added to wm to prevent paths from MTL structures to cortex 2165 additional wm voxels added 0 additional wm voxels added SEG EDIT: 87510 voxels turned on, 27344 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 37 found - 37 modified | TOTAL: 37 pass 2 (xy+): 0 found - 37 modified | TOTAL: 37 pass 1 (xy-): 29 found - 29 modified | TOTAL: 66 pass 2 (xy-): 0 found - 29 modified | TOTAL: 66 pass 1 (yz+): 50 found - 50 modified | TOTAL: 116 pass 2 (yz+): 0 found - 50 modified | TOTAL: 116 pass 1 (yz-): 37 found - 37 modified | TOTAL: 153 pass 2 (yz-): 0 found - 37 modified | TOTAL: 153 pass 1 (xz+): 22 found - 22 modified | TOTAL: 175 pass 2 (xz+): 0 found - 22 modified | TOTAL: 175 pass 1 (xz-): 25 found - 25 modified | TOTAL: 200 pass 2 (xz-): 0 found - 25 modified | TOTAL: 200 Iteration Number : 1 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 21 found - 21 modified | TOTAL: 31 pass 2 (+++): 0 found - 21 modified | TOTAL: 31 pass 1 (+++): 23 found - 23 modified | TOTAL: 54 pass 2 (+++): 0 found - 23 modified | TOTAL: 54 pass 1 (+++): 16 found - 16 modified | TOTAL: 70 pass 2 (+++): 0 found - 16 modified | TOTAL: 70 Iteration Number : 1 pass 1 (++): 96 found - 96 modified | TOTAL: 96 pass 2 (++): 0 found - 96 modified | TOTAL: 96 pass 1 (+-): 96 found - 96 modified | TOTAL: 192 pass 2 (+-): 1 found - 97 modified | TOTAL: 193 pass 3 (+-): 0 found - 97 modified | TOTAL: 193 pass 1 (--): 101 found - 101 modified | TOTAL: 294 pass 2 (--): 0 found - 101 modified | TOTAL: 294 pass 1 (-+): 81 found - 81 modified | TOTAL: 375 pass 2 (-+): 0 found - 81 modified | TOTAL: 375 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 5 found - 5 modified | TOTAL: 10 pass 2 (xy-): 0 found - 5 modified | TOTAL: 10 pass 1 (yz+): 2 found - 2 modified | TOTAL: 12 pass 2 (yz+): 0 found - 2 modified | TOTAL: 12 pass 1 (yz-): 6 found - 6 modified | TOTAL: 18 pass 2 (yz-): 0 found - 6 modified | TOTAL: 18 pass 1 (xz+): 6 found - 6 modified | TOTAL: 24 pass 2 (xz+): 0 found - 6 modified | TOTAL: 24 pass 1 (xz-): 5 found - 5 modified | TOTAL: 29 pass 2 (xz-): 0 found - 5 modified | TOTAL: 29 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 2 found - 2 modified | TOTAL: 9 pass 2 (--): 0 found - 2 modified | TOTAL: 9 pass 1 (-+): 2 found - 2 modified | TOTAL: 11 pass 2 (-+): 0 found - 2 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 696 (out of 516424: 0.134773) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Sat May 21 16:50:01 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.064 -0.030 -0.010 -6.232; 0.026 1.253 0.092 -31.927; 0.009 -0.091 0.995 -0.919; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1584 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) need search nearby using seed (125, 105, 91), TAL = (3.0, -37.0, 23.0) talairach voxel to voxel transform 0.939 0.023 0.008 6.599; -0.019 0.792 -0.074 25.113; -0.010 0.072 0.998 3.164; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 105, 91) --> (3.0, -37.0, 23.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (3.00, -37.00, 23.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -37.00, 23.00) SRC: (110.22, 99.60, 100.49) search lh wm seed point around talairach space (-15.00, -37.00, 23.00), SRC: (144.04, 98.93, 100.13) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat May 21 16:50:58 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 2 found - 2 modified | TOTAL: 4 pass 2 (xz+): 0 found - 2 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 247675: 0.002423) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 40: 1029 vertices, 1128 faces slice 50: 5487 vertices, 5709 faces slice 60: 12017 vertices, 12231 faces slice 70: 20002 vertices, 20358 faces slice 80: 28948 vertices, 29265 faces slice 90: 37797 vertices, 38081 faces slice 100: 47174 vertices, 47554 faces slice 110: 58831 vertices, 59196 faces slice 120: 69881 vertices, 70291 faces slice 130: 80337 vertices, 80701 faces slice 140: 90291 vertices, 90672 faces slice 150: 99092 vertices, 99387 faces slice 160: 106335 vertices, 106613 faces slice 170: 113180 vertices, 113423 faces slice 180: 119151 vertices, 119342 faces slice 190: 123302 vertices, 123452 faces slice 200: 125122 vertices, 125157 faces slice 210: 125140 vertices, 125166 faces slice 220: 125140 vertices, 125166 faces slice 230: 125140 vertices, 125166 faces slice 240: 125140 vertices, 125166 faces slice 250: 125140 vertices, 125166 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 125140 voxel in cpt #1: X=-26 [v=125140,e=375498,f=250332] located at (-27.166342, -14.946755, 24.110516) For the whole surface: X=-26 [v=125140,e=375498,f=250332] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat May 21 16:51:08 EDT 2011 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Sat May 21 16:51:13 EDT 2011 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts avg radius = 45.9 mm, total surface area = 66142 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Sat May 21 16:51:56 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.58 (0.00-->6.64) (max @ vno 44758 --> 44759) face area 0.03 +- 0.03 (-0.05-->0.53) scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.267, avgs=0 005/300: dt: 0.9000, rms radial error=177.008, avgs=0 010/300: dt: 0.9000, rms radial error=176.450, avgs=0 015/300: dt: 0.9000, rms radial error=175.716, avgs=0 020/300: dt: 0.9000, rms radial error=174.882, avgs=0 025/300: dt: 0.9000, rms radial error=173.990, avgs=0 030/300: dt: 0.9000, rms radial error=173.065, avgs=0 035/300: dt: 0.9000, rms radial error=172.123, avgs=0 040/300: dt: 0.9000, rms radial error=171.174, avgs=0 045/300: dt: 0.9000, rms radial error=170.222, avgs=0 050/300: dt: 0.9000, rms radial error=169.272, avgs=0 055/300: dt: 0.9000, rms radial error=168.324, avgs=0 060/300: dt: 0.9000, rms radial error=167.380, avgs=0 065/300: dt: 0.9000, rms radial error=166.439, avgs=0 070/300: dt: 0.9000, rms radial error=165.504, avgs=0 075/300: dt: 0.9000, rms radial error=164.573, avgs=0 080/300: dt: 0.9000, rms radial error=163.648, avgs=0 085/300: dt: 0.9000, rms radial error=162.727, avgs=0 090/300: dt: 0.9000, rms radial error=161.811, avgs=0 095/300: dt: 0.9000, rms radial error=160.900, avgs=0 100/300: dt: 0.9000, rms radial error=159.994, avgs=0 105/300: dt: 0.9000, rms radial error=159.093, avgs=0 110/300: dt: 0.9000, rms radial error=158.196, avgs=0 115/300: dt: 0.9000, rms radial error=157.305, avgs=0 120/300: dt: 0.9000, rms radial error=156.418, avgs=0 125/300: dt: 0.9000, rms radial error=155.536, avgs=0 130/300: dt: 0.9000, rms radial error=154.659, avgs=0 135/300: dt: 0.9000, rms radial error=153.786, avgs=0 140/300: dt: 0.9000, rms radial error=152.920, avgs=0 145/300: dt: 0.9000, rms radial error=152.058, avgs=0 150/300: dt: 0.9000, rms radial error=151.201, avgs=0 155/300: dt: 0.9000, rms radial error=150.350, avgs=0 160/300: dt: 0.9000, rms radial error=149.505, avgs=0 165/300: dt: 0.9000, rms radial error=148.665, avgs=0 170/300: dt: 0.9000, rms radial error=147.829, avgs=0 175/300: dt: 0.9000, rms radial error=146.998, avgs=0 180/300: dt: 0.9000, rms radial error=146.171, avgs=0 185/300: dt: 0.9000, rms radial error=145.349, avgs=0 190/300: dt: 0.9000, rms radial error=144.531, avgs=0 195/300: dt: 0.9000, rms radial error=143.718, avgs=0 200/300: dt: 0.9000, rms radial error=142.909, avgs=0 205/300: dt: 0.9000, rms radial error=142.104, avgs=0 210/300: dt: 0.9000, rms radial error=141.304, avgs=0 215/300: dt: 0.9000, rms radial error=140.509, avgs=0 220/300: dt: 0.9000, rms radial error=139.718, avgs=0 225/300: dt: 0.9000, rms radial error=138.931, avgs=0 230/300: dt: 0.9000, rms radial error=138.149, avgs=0 235/300: dt: 0.9000, rms radial error=137.371, avgs=0 240/300: dt: 0.9000, rms radial error=136.597, avgs=0 245/300: dt: 0.9000, rms radial error=135.828, avgs=0 250/300: dt: 0.9000, rms radial error=135.063, avgs=0 255/300: dt: 0.9000, rms radial error=134.302, avgs=0 260/300: dt: 0.9000, rms radial error=133.546, avgs=0 265/300: dt: 0.9000, rms radial error=132.793, avgs=0 270/300: dt: 0.9000, rms radial error=132.045, avgs=0 275/300: dt: 0.9000, rms radial error=131.301, avgs=0 280/300: dt: 0.9000, rms radial error=130.561, avgs=0 285/300: dt: 0.9000, rms radial error=129.826, avgs=0 290/300: dt: 0.9000, rms radial error=129.094, avgs=0 295/300: dt: 0.9000, rms radial error=128.367, avgs=0 300/300: dt: 0.9000, rms radial error=127.643, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14505.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2368.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 3 (K=160.0), pass 1, starting sse = 233.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00913 epoch 4 (K=640.0), pass 1, starting sse = 12.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/14 = 0.00852 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Sat May 21 16:57:09 EDT 2011 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 good_output lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-26 (nv=125140, nf=250332, ne=375498, g=14) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 2480 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 3 25 defects to be corrected 0 vertices coincident reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4919 (-4.7460) -vertex loglikelihood: -6.5836 (-3.2918) -normal dot loglikelihood: -3.5977 (-3.5977) -quad curv loglikelihood: -6.5515 (-3.2757) Total Loglikelihood : -26.2247 CORRECTING DEFECT 0 (vertices=31, convex hull=65) After retessellation of defect 0, euler #=-23 (123635,370361,246703) : difference with theory (-22) = 1 CORRECTING DEFECT 1 (vertices=32, convex hull=77) After retessellation of defect 1, euler #=-22 (123653,370448,246773) : difference with theory (-21) = 1 CORRECTING DEFECT 2 (vertices=73, convex hull=91) After retessellation of defect 2, euler #=-21 (123698,370627,246908) : difference with theory (-20) = 1 CORRECTING DEFECT 3 (vertices=33, convex hull=41) After retessellation of defect 3, euler #=-19 (123701,370651,246931) : difference with theory (-19) = 0 CORRECTING DEFECT 4 (vertices=121, convex hull=151) After retessellation of defect 4, euler #=-18 (123728,370800,247054) : difference with theory (-18) = 0 CORRECTING DEFECT 5 (vertices=34, convex hull=66) After retessellation of defect 5, euler #=-17 (123749,370888,247122) : difference with theory (-17) = 0 CORRECTING DEFECT 6 (vertices=46, convex hull=73) After retessellation of defect 6, euler #=-16 (123768,370973,247189) : difference with theory (-16) = 0 CORRECTING DEFECT 7 (vertices=45, convex hull=35) After retessellation of defect 7, euler #=-15 (123773,371001,247213) : difference with theory (-15) = 0 CORRECTING DEFECT 8 (vertices=31, convex hull=61) After retessellation of defect 8, euler #=-14 (123791,371079,247274) : difference with theory (-14) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=22) After retessellation of defect 9, euler #=-13 (123792,371089,247284) : difference with theory (-13) = 0 CORRECTING DEFECT 10 (vertices=96, convex hull=37) After retessellation of defect 10, euler #=-12 (123801,371127,247314) : difference with theory (-12) = 0 CORRECTING DEFECT 11 (vertices=11, convex hull=15) After retessellation of defect 11, euler #=-11 (123803,371137,247323) : difference with theory (-11) = 0 CORRECTING DEFECT 12 (vertices=19, convex hull=58) After retessellation of defect 12, euler #=-10 (123815,371195,247370) : difference with theory (-10) = 0 CORRECTING DEFECT 13 (vertices=42, convex hull=67) After retessellation of defect 13, euler #=-9 (123842,371301,247450) : difference with theory (-9) = 0 CORRECTING DEFECT 14 (vertices=498, convex hull=155) After retessellation of defect 14, euler #=-8 (123915,371599,247676) : difference with theory (-8) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=23) After retessellation of defect 15, euler #=-7 (123917,371612,247688) : difference with theory (-7) = 0 CORRECTING DEFECT 16 (vertices=40, convex hull=80) After retessellation of defect 16, euler #=-6 (123930,371680,247744) : difference with theory (-6) = 0 CORRECTING DEFECT 17 (vertices=9, convex hull=19) After retessellation of defect 17, euler #=-5 (123931,371688,247752) : difference with theory (-5) = 0 CORRECTING DEFECT 18 (vertices=34, convex hull=58) After retessellation of defect 18, euler #=-4 (123940,371740,247796) : difference with theory (-4) = 0 CORRECTING DEFECT 19 (vertices=10, convex hull=18) After retessellation of defect 19, euler #=-3 (123941,371748,247804) : difference with theory (-3) = 0 CORRECTING DEFECT 20 (vertices=180, convex hull=52) After retessellation of defect 20, euler #=-2 (123965,371839,247872) : difference with theory (-2) = 0 CORRECTING DEFECT 21 (vertices=53, convex hull=31) After retessellation of defect 21, euler #=-1 (123972,371872,247899) : difference with theory (-1) = 0 CORRECTING DEFECT 22 (vertices=19, convex hull=27) After retessellation of defect 22, euler #=0 (123975,371888,247913) : difference with theory (0) = 0 CORRECTING DEFECT 23 (vertices=15, convex hull=15) After retessellation of defect 23, euler #=1 (123977,371897,247921) : difference with theory (1) = 0 CORRECTING DEFECT 24 (vertices=30, convex hull=71) After retessellation of defect 24, euler #=2 (123985,371949,247966) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.09-->7.76) (max @ vno 32991 --> 33954) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.09-->7.76) (max @ vno 32991 --> 33954) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 88 mutations (35.9%), 157 crossovers (64.1%), 128 vertices were eliminated building final representation... 1155 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=123985, nf=247966, ne=371949, g=0) writing corrected surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.5 minutes 0 defective edges removing intersecting faces 000: 135 intersecting 001: 10 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 123985 - 371949 + 247966 = 2 --> 0 holes F =2V-4: 247966 = 247970-4 (0) 2E=3F: 743898 = 743898 (0) total defect index = 0 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 15 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat May 21 17:12:44 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs good_output lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11368 bright wm thresholded. 3520 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig... computing class statistics... border white: 234602 voxels (1.40%) border gray 265704 voxels (1.58%) WM (91.0): 92.7 +- 8.9 [70.0 --> 110.0] GM (78.0) : 75.5 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.2 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 35.4 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 22.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.84) (max @ vno 32991 --> 33954) face area 0.28 +- 0.12 (0.00-->2.16) mean absolute distance = 0.88 +- 1.05 3350 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=61 using class modes intead of means.... mean inside = 91.3, mean outside = 71.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=72.9, 176 (176) missing vertices, mean dist 0.5 [0.8 (%25.7)->0.9 (%74.3))] %56 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.28 (0.09-->4.38) (max @ vno 32991 --> 33954) face area 0.28 +- 0.14 (0.00-->2.64) mean absolute distance = 0.41 +- 0.72 2697 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6329051.0, rms=13.27 001: dt: 0.5000, sse=6197822.0, rms=10.00 002: dt: 0.5000, sse=6149266.0, rms=7.77 003: dt: 0.5000, sse=6326496.5, rms=6.20 004: dt: 0.5000, sse=6418171.5, rms=5.15 005: dt: 0.5000, sse=6638016.5, rms=4.51 006: dt: 0.5000, sse=6731400.0, rms=4.13 007: dt: 0.5000, sse=6869702.5, rms=3.92 008: dt: 0.5000, sse=6882630.0, rms=3.79 009: dt: 0.5000, sse=6935772.0, rms=3.71 rms = 3.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6924483.5, rms=3.66 011: dt: 0.2500, sse=4281181.0, rms=2.53 012: dt: 0.2500, sse=3911207.5, rms=2.20 013: dt: 0.2500, sse=3712769.5, rms=2.12 014: dt: 0.2500, sse=3681660.5, rms=2.06 rms = 2.04, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3618110.0, rms=2.04 016: dt: 0.1250, sse=3556364.2, rms=1.99 rms = 1.98, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3534903.2, rms=1.98 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=76.6, 218 (106) missing vertices, mean dist -0.3 [0.5 (%71.2)->0.3 (%28.8))] %66 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.09-->4.32) (max @ vno 98332 --> 95316) face area 0.36 +- 0.17 (0.00-->3.51) mean absolute distance = 0.31 +- 0.45 2683 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4267467.0, rms=5.44 018: dt: 0.5000, sse=4595683.5, rms=3.43 rms = 3.56, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=4222512.0, rms=2.68 020: dt: 0.2500, sse=4034952.5, rms=2.09 021: dt: 0.2500, sse=3918147.8, rms=1.81 022: dt: 0.2500, sse=3862143.5, rms=1.71 rms = 1.66, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3821993.0, rms=1.66 024: dt: 0.1250, sse=3762290.5, rms=1.61 rms = 1.60, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3737991.0, rms=1.60 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=80.3, 210 (92) missing vertices, mean dist -0.2 [0.3 (%74.4)->0.2 (%25.6))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.07-->4.27) (max @ vno 32991 --> 33954) face area 0.35 +- 0.17 (0.00-->3.32) mean absolute distance = 0.24 +- 0.35 2707 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4161232.0, rms=4.63 026: dt: 0.5000, sse=4368176.0, rms=3.12 rms = 3.43, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4053769.0, rms=2.15 028: dt: 0.2500, sse=3949973.0, rms=1.68 029: dt: 0.2500, sse=3914751.2, rms=1.49 rms = 1.49, time step reduction 2 of 3 to 0.125... rms = 1.45, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3883770.8, rms=1.45 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.6, 211 (88) missing vertices, mean dist -0.1 [0.3 (%59.1)->0.2 (%40.9))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3928903.5, rms=2.17 rms = 2.38, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3970868.5, rms=1.49 032: dt: 0.2500, sse=4139708.2, rms=1.09 rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4134702.5, rms=1.07 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 18 non-cortical segments detected only using segment with 1916 vertices erasing segment 1 (vno[0] = 48904) erasing segment 2 (vno[0] = 67052) erasing segment 3 (vno[0] = 73515) erasing segment 4 (vno[0] = 75322) erasing segment 5 (vno[0] = 87121) erasing segment 6 (vno[0] = 88321) erasing segment 7 (vno[0] = 89236) erasing segment 8 (vno[0] = 92154) erasing segment 9 (vno[0] = 92155) erasing segment 10 (vno[0] = 93754) erasing segment 11 (vno[0] = 95316) erasing segment 12 (vno[0] = 98302) erasing segment 13 (vno[0] = 98335) erasing segment 14 (vno[0] = 100365) erasing segment 15 (vno[0] = 101140) erasing segment 16 (vno[0] = 101906) erasing segment 17 (vno[0] = 123904) writing cortex label to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.cortex.label... LabelWrite: saving to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.cortex.label writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.area vertex spacing 0.91 +- 0.26 (0.05-->4.22) (max @ vno 32991 --> 33954) face area 0.34 +- 0.17 (0.00-->3.23) refinement took 5.8 minutes #-------------------------------------------- #@# Smooth2 lh Sat May 21 17:18:33 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Sat May 21 17:18:38 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.1 mm, total surface area = 77595 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 274 vertices thresholded to be in k1 ~ [-0.25 0.41], k2 ~ [-0.11 0.07] total integrated curvature = 0.568*4pi (7.138) --> 0 handles ICI = 1.5, FI = 9.1, variation=158.334 147 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 135 vertices thresholded to be in [-0.15 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #-------------------------------------------- #@# Sphere lh Sat May 21 17:20:42 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 0.93 hours scaling brain by 0.293... pass 1: epoch 1 of 3 starting distance error %19.23 pass 1: epoch 2 of 3 starting distance error %19.23 unfolding complete - removing small folds... starting distance error %19.15 removing remaining folds... final distance error %19.16 #-------------------------------------------- #@# Surf Reg lh Sat May 21 18:16:41 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_register -curv ../surf/lh.sphere /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.583 curvature mean = 0.036, std = 0.937 curvature mean = 0.020, std = 0.869 curvature mean = 0.027, std = 0.968 curvature mean = 0.009, std = 0.944 curvature mean = 0.027, std = 0.981 curvature mean = 0.004, std = 0.974 curvature mean = 0.027, std = 0.984 curvature mean = 0.001, std = 0.989 curvature mean = -0.025, std = 0.285 curvature mean = 0.005, std = 0.068 curvature mean = 0.063, std = 0.355 curvature mean = 0.004, std = 0.080 curvature mean = 0.030, std = 0.550 curvature mean = 0.004, std = 0.086 curvature mean = 0.017, std = 0.687 curvature mean = 0.005, std = 0.088 curvature mean = 0.006, std = 0.792 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sat May 21 18:51:35 EDT 2011 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Sat May 21 18:51:38 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mrisp_paint -a 5 /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sat May 21 18:51:41 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1148 labels changed using aseg relabeling using gibbs priors... 000: 2766 changed, 123985 examined... 001: 645 changed, 12002 examined... 002: 155 changed, 3638 examined... 003: 59 changed, 895 examined... 004: 23 changed, 357 examined... 005: 11 changed, 136 examined... 006: 2 changed, 67 examined... 007: 1 changed, 13 examined... 008: 0 changed, 9 examined... 215 labels changed using aseg 000: 122 total segments, 77 labels (263 vertices) changed 001: 43 total segments, 2 labels (11 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 16 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1853 vertices marked for relabeling... 1853 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 52 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat May 21 18:52:33 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs good_output lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11368 bright wm thresholded. 3520 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig... computing class statistics... border white: 234602 voxels (1.40%) border gray 265704 voxels (1.58%) WM (91.0): 92.7 +- 8.9 [70.0 --> 110.0] GM (78.0) : 75.5 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.2 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 35.4 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 22.6 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=61 using class modes intead of means.... mean inside = 91.3, mean outside = 71.2 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.84) (max @ vno 32991 --> 33954) face area 0.28 +- 0.12 (0.00-->2.16) mean absolute distance = 0.89 +- 1.06 3440 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 462 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown mean border=72.9, 176 (176) missing vertices, mean dist 0.4 [0.9 (%25.6)->0.9 (%74.4))] %56 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.28 (0.09-->4.38) (max @ vno 32991 --> 33954) face area 0.28 +- 0.14 (0.00-->2.64) mean absolute distance = 0.41 +- 0.72 2730 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6344510.5, rms=13.26 001: dt: 0.5000, sse=6212005.0, rms=9.99 002: dt: 0.5000, sse=6162029.0, rms=7.77 003: dt: 0.5000, sse=6341541.5, rms=6.20 004: dt: 0.5000, sse=6433680.0, rms=5.14 005: dt: 0.5000, sse=6655411.0, rms=4.50 006: dt: 0.5000, sse=6752219.0, rms=4.13 007: dt: 0.5000, sse=6892986.0, rms=3.91 008: dt: 0.5000, sse=6908418.5, rms=3.79 009: dt: 0.5000, sse=6961209.0, rms=3.71 rms = 3.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6945649.5, rms=3.66 011: dt: 0.2500, sse=4294394.5, rms=2.52 012: dt: 0.2500, sse=3922750.0, rms=2.20 013: dt: 0.2500, sse=3723880.0, rms=2.12 014: dt: 0.2500, sse=3692863.0, rms=2.06 rms = 2.04, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3629572.2, rms=2.04 016: dt: 0.1250, sse=3567820.2, rms=1.99 rms = 1.98, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3546420.2, rms=1.98 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 5 with 250 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 34 points - only 26.47% unknown deleting segment 10 with 36 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=76.6, 222 (106) missing vertices, mean dist -0.3 [0.5 (%71.2)->0.3 (%28.8))] %66 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.09-->4.32) (max @ vno 98332 --> 95316) face area 0.36 +- 0.17 (0.00-->3.51) mean absolute distance = 0.31 +- 0.45 2706 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4282216.0, rms=5.43 018: dt: 0.5000, sse=4613386.0, rms=3.43 rms = 3.56, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=4239092.5, rms=2.68 020: dt: 0.2500, sse=4052016.5, rms=2.09 021: dt: 0.2500, sse=3935484.5, rms=1.81 022: dt: 0.2500, sse=3878903.5, rms=1.71 rms = 1.66, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3838821.0, rms=1.66 024: dt: 0.1250, sse=3779459.0, rms=1.61 rms = 1.60, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3755451.0, rms=1.60 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 33.33% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 287 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 35 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=80.3, 214 (92) missing vertices, mean dist -0.2 [0.3 (%74.4)->0.2 (%25.6))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.26 (0.07-->4.27) (max @ vno 32991 --> 33954) face area 0.35 +- 0.17 (0.00-->3.32) mean absolute distance = 0.24 +- 0.35 2741 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4180486.8, rms=4.63 026: dt: 0.5000, sse=4383051.0, rms=3.12 rms = 3.42, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4069119.2, rms=2.15 028: dt: 0.2500, sse=3965888.2, rms=1.68 029: dt: 0.2500, sse=3932263.0, rms=1.49 rms = 1.49, time step reduction 2 of 3 to 0.125... rms = 1.45, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3901276.2, rms=1.45 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 351 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 57 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=81.6, 213 (88) missing vertices, mean dist -0.1 [0.3 (%59.1)->0.2 (%40.9))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3946272.5, rms=2.16 rms = 2.38, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3988847.8, rms=1.49 032: dt: 0.2500, sse=4159365.0, rms=1.09 rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4154275.2, rms=1.07 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=51.0, 182 (182) missing vertices, mean dist 1.9 [2.8 (%0.0)->2.2 (%100.0))] %21 local maxima, %60 large gradients and %14 min vals, 927 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=24012604.0, rms=30.24 001: dt: 0.5000, sse=17883644.0, rms=25.57 002: dt: 0.5000, sse=13399743.0, rms=21.55 003: dt: 0.5000, sse=10322144.0, rms=18.22 004: dt: 0.5000, sse=8492365.0, rms=15.49 005: dt: 0.5000, sse=7412448.5, rms=13.22 006: dt: 0.5000, sse=6738608.5, rms=11.34 007: dt: 0.5000, sse=6251581.5, rms=9.71 008: dt: 0.5000, sse=5987986.0, rms=8.28 009: dt: 0.5000, sse=5834694.0, rms=7.06 010: dt: 0.5000, sse=5813944.0, rms=6.09 011: dt: 0.5000, sse=5846632.5, rms=5.37 012: dt: 0.5000, sse=5935385.0, rms=4.88 013: dt: 0.5000, sse=5973367.5, rms=4.55 014: dt: 0.5000, sse=6063074.0, rms=4.33 015: dt: 0.5000, sse=6085752.0, rms=4.19 016: dt: 0.5000, sse=6125721.5, rms=4.08 017: dt: 0.5000, sse=6126597.5, rms=4.02 018: dt: 0.5000, sse=6132139.0, rms=3.96 rms = 3.92, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6117995.0, rms=3.92 020: dt: 0.2500, sse=4088313.5, rms=3.06 021: dt: 0.2500, sse=3860314.5, rms=2.85 rms = 2.81, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3736192.8, rms=2.81 023: dt: 0.1250, sse=3585934.0, rms=2.69 rms = 2.67, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3563505.8, rms=2.67 positioning took 2.4 minutes mean border=48.2, 458 (38) missing vertices, mean dist 0.2 [0.2 (%46.0)->0.6 (%54.0))] %46 local maxima, %40 large gradients and % 8 min vals, 357 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4273872.0, rms=5.38 025: dt: 0.5000, sse=4488653.5, rms=4.10 026: dt: 0.5000, sse=5626501.5, rms=4.00 rms = 4.07, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4614480.0, rms=3.23 028: dt: 0.2500, sse=4258937.0, rms=2.91 029: dt: 0.2500, sse=4192420.8, rms=2.84 rms = 2.80, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4151152.5, rms=2.80 031: dt: 0.1250, sse=4024856.0, rms=2.68 rms = 2.66, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4008411.2, rms=2.66 positioning took 0.8 minutes mean border=45.6, 582 (19) missing vertices, mean dist 0.2 [0.2 (%38.1)->0.4 (%61.9))] %64 local maxima, %22 large gradients and % 8 min vals, 372 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4288465.0, rms=4.22 033: dt: 0.5000, sse=4461768.5, rms=3.90 rms = 3.94, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4185085.8, rms=3.10 035: dt: 0.2500, sse=4284203.5, rms=2.78 036: dt: 0.2500, sse=4266806.0, rms=2.72 rms = 2.70, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4276490.5, rms=2.70 038: dt: 0.1250, sse=4164255.0, rms=2.57 rms = 2.55, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4153513.8, rms=2.55 positioning took 0.7 minutes mean border=44.2, 1206 (8) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))] %71 local maxima, %15 large gradients and % 8 min vals, 340 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4217216.0, rms=3.02 rms = 3.58, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4101834.0, rms=2.66 041: dt: 0.2500, sse=4191734.0, rms=2.51 rms = 2.46, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4261401.0, rms=2.46 043: dt: 0.1250, sse=4198931.5, rms=2.37 rms = 2.34, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4193945.2, rms=2.34 positioning took 0.5 minutes writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.area.pial vertex spacing 1.02 +- 0.42 (0.10-->6.28) (max @ vno 86303 --> 85324) face area 0.41 +- 0.30 (0.00-->5.68) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 123985 vertices processed 25000 of 123985 vertices processed 50000 of 123985 vertices processed 75000 of 123985 vertices processed 100000 of 123985 vertices processed 0 of 123985 vertices processed 25000 of 123985 vertices processed 50000 of 123985 vertices processed 75000 of 123985 vertices processed 100000 of 123985 vertices processed thickness calculation complete, 399:516 truncations. 52460 vertices at 0 distance 80653 vertices at 1 distance 66066 vertices at 2 distance 24086 vertices at 3 distance 7424 vertices at 4 distance 2456 vertices at 5 distance 1066 vertices at 6 distance 547 vertices at 7 distance 266 vertices at 8 distance 153 vertices at 9 distance 99 vertices at 10 distance 79 vertices at 11 distance 52 vertices at 12 distance 38 vertices at 13 distance 35 vertices at 14 distance 24 vertices at 15 distance 19 vertices at 16 distance 11 vertices at 17 distance 9 vertices at 18 distance 6 vertices at 19 distance 15 vertices at 20 distance writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.thickness positioning took 10.8 minutes #-------------------------------------------- #@# Surf Volume lh Sat May 21 19:03:20 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Sat May 21 19:03:23 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab good_output lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1694 1187 2796 2.373 0.444 0.112 0.029 13 2.0 bankssts 900 592 1502 2.523 0.587 0.150 0.073 35 2.1 caudalanteriorcingulate 2930 1971 5294 2.460 0.534 0.136 0.049 36 5.6 caudalmiddlefrontal 1769 1191 2219 1.654 0.407 0.156 0.065 31 4.0 cuneus 484 347 1675 3.382 0.694 0.140 0.045 6 0.9 entorhinal 4287 3038 8717 2.503 0.700 0.150 0.051 74 9.1 fusiform 6258 4373 11128 2.324 0.499 0.146 0.075 138 14.9 inferiorparietal 4897 3401 10817 2.770 0.722 0.170 0.082 121 15.9 inferiortemporal 1393 927 2457 2.446 0.854 0.157 0.061 27 3.5 isthmuscingulate 5518 3779 8645 2.054 0.535 0.154 0.057 88 11.9 lateraloccipital 3068 2192 6158 2.439 0.601 0.168 0.077 69 8.3 lateralorbitofrontal 3748 2693 5456 1.862 0.579 0.153 0.054 62 8.3 lingual 3140 2120 5733 2.307 0.840 0.156 0.101 117 10.1 medialorbitofrontal 4466 3191 10150 2.699 0.605 0.162 0.068 123 11.9 middletemporal 1196 775 1746 1.900 0.611 0.095 0.027 8 1.6 parahippocampal 1862 1221 3125 2.300 0.513 0.128 0.045 19 3.4 paracentral 2162 1486 3861 2.333 0.447 0.141 0.046 32 4.0 parsopercularis 825 562 1697 2.411 0.519 0.154 0.060 14 1.8 parsorbitalis 1704 1196 3030 2.252 0.479 0.145 0.051 24 3.5 parstriangularis 1336 899 1204 1.469 0.419 0.134 0.045 16 2.6 pericalcarine 6272 4189 9122 1.975 0.573 0.135 0.066 81 12.9 postcentral 1599 1134 3014 2.401 0.717 0.174 0.099 75 5.9 posteriorcingulate 6816 4446 12122 2.502 0.491 0.125 0.202 140 17.0 precentral 5231 3688 9615 2.385 0.593 0.158 0.061 90 12.3 precuneus 1212 826 2594 2.690 0.545 0.166 0.073 34 3.2 rostralanteriorcingulate 6816 4785 12746 2.271 0.547 0.164 0.070 141 18.5 rostralmiddlefrontal 8767 6225 18368 2.554 0.630 0.147 0.057 122 20.4 superiorfrontal 7561 5198 12514 2.192 0.549 0.146 0.063 149 20.0 superiorparietal 6184 4158 11388 2.387 0.625 0.135 0.060 109 13.4 superiortemporal 6149 4224 11809 2.473 0.533 0.161 0.069 210 18.6 supramarginal 257 191 748 2.709 0.485 0.192 0.129 11 1.0 frontalpole 701 488 2330 3.409 0.674 0.146 0.050 9 1.5 temporalpole 644 395 1156 2.535 0.442 0.142 0.079 14 2.2 transversetemporal 3563 2347 6538 2.668 0.867 0.126 0.086 68 9.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat May 21 19:03:38 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 20 labels changed using aseg relabeling using gibbs priors... 000: 8740 changed, 123985 examined... 001: 2085 changed, 33358 examined... 002: 636 changed, 10755 examined... 003: 275 changed, 3531 examined... 004: 125 changed, 1476 examined... 005: 84 changed, 722 examined... 006: 41 changed, 462 examined... 007: 14 changed, 209 examined... 008: 2 changed, 76 examined... 009: 3 changed, 16 examined... 010: 0 changed, 15 examined... 11 labels changed using aseg 000: 266 total segments, 180 labels (1957 vertices) changed 001: 93 total segments, 7 labels (26 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 125 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1091 vertices marked for relabeling... 1091 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 58 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat May 21 19:04:36 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab good_output lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1259 871 2257 2.211 0.618 0.166 0.083 28 3.8 G_and_S_frontomargin 1308 893 2346 2.209 0.626 0.146 0.047 20 2.4 G_and_S_occipital_inf 1391 927 2505 2.215 0.504 0.144 0.091 58 6.3 G_and_S_paracentral 1441 989 3021 2.580 0.542 0.157 0.063 24 3.3 G_and_S_subcentral 658 479 1445 2.317 0.586 0.196 0.103 23 2.5 G_and_S_transv_frontopol 2376 1613 4278 2.408 0.530 0.140 0.051 32 4.8 G_and_S_cingul-Ant 1069 745 1925 2.402 0.520 0.131 0.040 13 1.7 G_and_S_cingul-Mid-Ant 1167 837 2212 2.454 0.570 0.153 0.086 23 2.7 G_and_S_cingul-Mid-Post 487 353 1333 2.924 0.604 0.205 0.086 14 1.6 G_cingul-Post-dorsal 332 192 404 1.973 0.806 0.150 0.083 9 1.3 G_cingul-Post-ventral 1500 1041 2088 1.686 0.389 0.170 0.062 28 4.0 G_cuneus 1294 862 2732 2.495 0.418 0.148 0.069 22 2.8 G_front_inf-Opercular 366 237 890 2.827 0.461 0.191 0.085 10 1.1 G_front_inf-Orbital 1021 737 2171 2.350 0.449 0.171 0.070 23 2.8 G_front_inf-Triangul 3485 2425 7746 2.509 0.557 0.173 0.076 79 10.5 G_front_middle 6369 4479 14826 2.716 0.599 0.161 0.074 125 18.3 G_front_sup 565 350 1187 2.747 0.637 0.121 0.090 12 1.1 G_Ins_lg_and_S_cent_ins 703 462 1955 3.155 0.817 0.163 0.189 26 3.2 G_insular_short 1547 1088 3299 2.450 0.435 0.169 0.064 32 4.0 G_occipital_middle 1636 1111 2424 1.974 0.463 0.167 0.065 29 3.5 G_occipital_sup 1817 1238 4105 2.612 0.660 0.154 0.053 36 4.1 G_oc-temp_lat-fusifor 2621 1822 3892 1.829 0.608 0.161 0.058 48 6.3 G_oc-temp_med-Lingual 1047 696 2506 2.602 0.935 0.115 0.054 17 2.5 G_oc-temp_med-Parahip 2105 1505 4906 2.478 0.608 0.188 0.094 62 6.9 G_orbital 1970 1359 4327 2.515 0.534 0.179 0.142 85 7.1 G_pariet_inf-Angular 3611 2481 7579 2.505 0.543 0.168 0.078 173 11.8 G_pariet_inf-Supramar 2746 1914 5734 2.473 0.474 0.163 0.088 86 11.6 G_parietal_sup 2333 1518 3562 1.966 0.478 0.141 0.106 37 6.1 G_postcentral 2378 1505 5228 2.709 0.434 0.138 0.061 39 6.0 G_precentral 2700 1932 6089 2.550 0.554 0.183 0.082 65 8.5 G_precuneus 1080 786 2585 2.511 0.739 0.183 0.102 39 4.2 G_rectus 382 229 617 2.505 0.809 0.187 0.280 58 2.4 G_subcallosal 501 292 948 2.511 0.416 0.136 0.092 13 2.0 G_temp_sup-G_T_transv 2398 1633 5065 2.413 0.664 0.147 0.072 48 6.7 G_temp_sup-Lateral 768 515 1772 2.924 0.814 0.125 0.113 15 1.7 G_temp_sup-Plan_polar 997 706 1967 2.446 0.456 0.144 0.048 15 2.3 G_temp_sup-Plan_tempo 2977 2096 7768 2.898 0.759 0.197 0.110 105 13.4 G_temporal_inf 2834 2069 7246 2.814 0.570 0.183 0.083 106 9.3 G_temporal_middle 309 207 416 2.029 0.426 0.102 0.019 2 0.2 Lat_Fis-ant-Horizont 272 193 335 1.870 0.382 0.127 0.030 2 0.4 Lat_Fis-ant-Vertical 1302 869 1593 2.230 0.485 0.121 0.034 10 1.9 Lat_Fis-post 1720 1185 2336 1.751 0.473 0.162 0.062 27 4.2 Pole_occipital 1745 1230 5248 3.225 0.672 0.159 0.059 30 4.2 Pole_temporal 1507 1044 1721 1.742 0.698 0.135 0.045 18 2.7 S_calcarine 3104 2070 3541 1.938 0.604 0.108 0.341 27 4.6 S_central 990 701 1406 2.078 0.485 0.109 0.024 6 1.1 S_cingul-Marginalis 549 362 964 2.771 0.618 0.109 0.031 3 0.8 S_circular_insula_ant 1564 1036 2050 2.188 0.732 0.104 0.037 23 2.5 S_circular_insula_inf 1669 1109 2241 2.313 0.461 0.120 0.041 15 2.8 S_circular_insula_sup 783 552 1480 2.636 0.753 0.135 0.046 11 1.4 S_collat_transv_ant 324 231 366 1.863 0.421 0.137 0.036 3 0.5 S_collat_transv_post 1959 1347 3054 2.218 0.467 0.139 0.046 26 3.6 S_front_inf 905 643 1573 2.182 0.598 0.142 0.057 12 1.8 S_front_middle 2506 1756 3960 2.245 0.566 0.120 0.035 21 3.6 S_front_sup 405 283 634 2.467 0.569 0.166 0.092 7 2.1 S_interm_prim-Jensen 2240 1530 3039 2.121 0.576 0.125 0.045 23 3.3 S_intrapariet_and_P_trans 669 466 958 2.208 0.455 0.145 0.047 8 1.2 S_oc_middle_and_Lunatus 1237 835 1542 1.979 0.479 0.110 0.032 8 1.6 S_oc_sup_and_transversal 671 469 948 2.063 0.374 0.114 0.031 4 0.9 S_occipital_ant 767 546 1345 2.435 0.530 0.150 0.059 11 1.4 S_oc-temp_lat 2424 1757 3324 2.012 0.583 0.126 0.039 28 4.0 S_oc-temp_med_and_Lingual 382 260 530 2.143 0.357 0.121 0.035 2 0.6 S_orbital_lateral 968 658 1399 2.119 1.020 0.124 0.070 20 2.0 S_orbital_med-olfact 917 664 1605 2.311 0.573 0.163 0.067 15 2.5 S_orbital-H_Shaped 1797 1225 2325 2.072 0.677 0.143 0.056 24 3.4 S_parieto_occipital 1362 867 1745 2.430 0.897 0.158 0.086 84 4.9 S_pericallosal 3312 2215 4596 2.127 0.504 0.136 0.041 41 5.7 S_postcentral 1547 1064 2368 2.310 0.399 0.111 0.030 11 1.9 S_precentral-inf-part 830 598 1141 2.209 0.360 0.104 0.020 4 0.8 S_precentral-sup-part 515 357 833 2.248 0.829 0.159 0.050 8 1.0 S_suborbital 1120 778 1730 2.214 0.470 0.132 0.035 10 1.6 S_subparietal 1209 825 1767 2.411 0.516 0.121 0.032 9 1.6 S_temporal_inf 6266 4312 9929 2.316 0.491 0.123 0.038 72 9.8 S_temporal_sup 324 206 496 2.656 0.553 0.140 0.042 3 0.6 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Sat May 21 19:04:52 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 254949: 0.002353) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 40: 641 vertices, 701 faces slice 50: 4506 vertices, 4713 faces slice 60: 10825 vertices, 11042 faces slice 70: 18382 vertices, 18699 faces slice 80: 27324 vertices, 27618 faces slice 90: 35984 vertices, 36299 faces slice 100: 45324 vertices, 45688 faces slice 110: 56379 vertices, 56744 faces slice 120: 67107 vertices, 67507 faces slice 130: 77600 vertices, 77962 faces slice 140: 87467 vertices, 87844 faces slice 150: 97169 vertices, 97496 faces slice 160: 104569 vertices, 104849 faces slice 170: 111972 vertices, 112234 faces slice 180: 118477 vertices, 118674 faces slice 190: 123647 vertices, 123836 faces slice 200: 126629 vertices, 126686 faces slice 210: 126750 vertices, 126778 faces slice 220: 126750 vertices, 126778 faces slice 230: 126750 vertices, 126778 faces slice 240: 126750 vertices, 126778 faces slice 250: 126750 vertices, 126778 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 126750 voxel in cpt #1: X=-28 [v=126750,e=380334,f=253556] located at (27.614422, -11.854943, 24.574524) For the whole surface: X=-28 [v=126750,e=380334,f=253556] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sat May 21 19:05:03 EDT 2011 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Sat May 21 19:05:08 EDT 2011 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts avg radius = 46.7 mm, total surface area = 67381 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Sat May 21 19:05:51 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.57 (0.00-->5.49) (max @ vno 42910 --> 43940) face area 0.03 +- 0.03 (-0.03-->0.47) scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.069, avgs=0 005/300: dt: 0.9000, rms radial error=176.809, avgs=0 010/300: dt: 0.9000, rms radial error=176.250, avgs=0 015/300: dt: 0.9000, rms radial error=175.515, avgs=0 020/300: dt: 0.9000, rms radial error=174.678, avgs=0 025/300: dt: 0.9000, rms radial error=173.783, avgs=0 030/300: dt: 0.9000, rms radial error=172.860, avgs=0 035/300: dt: 0.9000, rms radial error=171.924, avgs=0 040/300: dt: 0.9000, rms radial error=170.979, avgs=0 045/300: dt: 0.9000, rms radial error=170.032, avgs=0 050/300: dt: 0.9000, rms radial error=169.086, avgs=0 055/300: dt: 0.9000, rms radial error=168.143, avgs=0 060/300: dt: 0.9000, rms radial error=167.202, avgs=0 065/300: dt: 0.9000, rms radial error=166.267, avgs=0 070/300: dt: 0.9000, rms radial error=165.335, avgs=0 075/300: dt: 0.9000, rms radial error=164.409, avgs=0 080/300: dt: 0.9000, rms radial error=163.487, avgs=0 085/300: dt: 0.9000, rms radial error=162.570, avgs=0 090/300: dt: 0.9000, rms radial error=161.658, avgs=0 095/300: dt: 0.9000, rms radial error=160.752, avgs=0 100/300: dt: 0.9000, rms radial error=159.850, avgs=0 105/300: dt: 0.9000, rms radial error=158.953, avgs=0 110/300: dt: 0.9000, rms radial error=158.061, avgs=0 115/300: dt: 0.9000, rms radial error=157.174, avgs=0 120/300: dt: 0.9000, rms radial error=156.292, avgs=0 125/300: dt: 0.9000, rms radial error=155.414, avgs=0 130/300: dt: 0.9000, rms radial error=154.542, avgs=0 135/300: dt: 0.9000, rms radial error=153.674, avgs=0 140/300: dt: 0.9000, rms radial error=152.810, avgs=0 145/300: dt: 0.9000, rms radial error=151.952, avgs=0 150/300: dt: 0.9000, rms radial error=151.098, avgs=0 155/300: dt: 0.9000, rms radial error=150.248, avgs=0 160/300: dt: 0.9000, rms radial error=149.404, avgs=0 165/300: dt: 0.9000, rms radial error=148.564, avgs=0 170/300: dt: 0.9000, rms radial error=147.729, avgs=0 175/300: dt: 0.9000, rms radial error=146.898, avgs=0 180/300: dt: 0.9000, rms radial error=146.071, avgs=0 185/300: dt: 0.9000, rms radial error=145.250, avgs=0 190/300: dt: 0.9000, rms radial error=144.432, avgs=0 195/300: dt: 0.9000, rms radial error=143.620, avgs=0 200/300: dt: 0.9000, rms radial error=142.811, avgs=0 205/300: dt: 0.9000, rms radial error=142.007, avgs=0 210/300: dt: 0.9000, rms radial error=141.208, avgs=0 215/300: dt: 0.9000, rms radial error=140.413, avgs=0 220/300: dt: 0.9000, rms radial error=139.622, avgs=0 225/300: dt: 0.9000, rms radial error=138.836, avgs=0 230/300: dt: 0.9000, rms radial error=138.054, avgs=0 235/300: dt: 0.9000, rms radial error=137.276, avgs=0 240/300: dt: 0.9000, rms radial error=136.503, avgs=0 245/300: dt: 0.9000, rms radial error=135.734, avgs=0 250/300: dt: 0.9000, rms radial error=134.969, avgs=0 255/300: dt: 0.9000, rms radial error=134.208, avgs=0 260/300: dt: 0.9000, rms radial error=133.452, avgs=0 265/300: dt: 0.9000, rms radial error=132.700, avgs=0 270/300: dt: 0.9000, rms radial error=131.952, avgs=0 275/300: dt: 0.9000, rms radial error=131.208, avgs=0 280/300: dt: 0.9000, rms radial error=130.468, avgs=0 285/300: dt: 0.9000, rms radial error=129.733, avgs=0 290/300: dt: 0.9000, rms radial error=129.002, avgs=0 295/300: dt: 0.9000, rms radial error=128.274, avgs=0 300/300: dt: 0.9000, rms radial error=127.551, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14715.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 2 (K=40.0), pass 1, starting sse = 2399.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 238.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/15 = 0.01036 epoch 4 (K=640.0), pass 1, starting sse = 11.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.30/25 = 0.01208 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.11 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sat May 21 19:12:10 EDT 2011 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 good_output rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-28 (nv=126750, nf=253556, ne=380334, g=15) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 1825 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4497 (-4.7248) -vertex loglikelihood: -6.4838 (-3.2419) -normal dot loglikelihood: -3.6126 (-3.6126) -quad curv loglikelihood: -6.4810 (-3.2405) Total Loglikelihood : -26.0271 CORRECTING DEFECT 0 (vertices=29, convex hull=69) After retessellation of defect 0, euler #=-23 (125603,376316,250690) : difference with theory (-23) = 0 CORRECTING DEFECT 1 (vertices=48, convex hull=52) After retessellation of defect 1, euler #=-22 (125627,376409,250760) : difference with theory (-22) = 0 CORRECTING DEFECT 2 (vertices=43, convex hull=32) After retessellation of defect 2, euler #=-21 (125634,376439,250784) : difference with theory (-21) = 0 CORRECTING DEFECT 3 (vertices=5, convex hull=25) After retessellation of defect 3, euler #=-20 (125636,376452,250796) : difference with theory (-20) = 0 CORRECTING DEFECT 4 (vertices=31, convex hull=59) After retessellation of defect 4, euler #=-19 (125656,376533,250858) : difference with theory (-19) = 0 CORRECTING DEFECT 5 (vertices=41, convex hull=73) After retessellation of defect 5, euler #=-18 (125670,376605,250917) : difference with theory (-18) = 0 CORRECTING DEFECT 6 (vertices=29, convex hull=54) After retessellation of defect 6, euler #=-17 (125684,376673,250972) : difference with theory (-17) = 0 CORRECTING DEFECT 7 (vertices=16, convex hull=44) After retessellation of defect 7, euler #=-16 (125693,376718,251009) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=51, convex hull=78) After retessellation of defect 8, euler #=-15 (125724,376844,251105) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=7, convex hull=16) After retessellation of defect 9, euler #=-14 (125726,376853,251113) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=18, convex hull=15) After retessellation of defect 10, euler #=-13 (125727,376859,251119) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=10, convex hull=24) After retessellation of defect 11, euler #=-12 (125728,376870,251130) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=71, convex hull=26) After retessellation of defect 12, euler #=-11 (125737,376906,251158) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=53, convex hull=80) After retessellation of defect 13, euler #=-10 (125758,377001,251233) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=51, convex hull=81) After retessellation of defect 14, euler #=-9 (125770,377067,251288) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=62, convex hull=33) After retessellation of defect 15, euler #=-8 (125776,377095,251311) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=41, convex hull=40) After retessellation of defect 16, euler #=-7 (125781,377128,251340) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=40, convex hull=17) After retessellation of defect 17, euler #=-6 (125781,377131,251344) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=9, convex hull=23) After retessellation of defect 18, euler #=-5 (125783,377146,251358) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=182, convex hull=63) After retessellation of defect 19, euler #=-4 (125804,377237,251429) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=40, convex hull=71) After retessellation of defect 20, euler #=-3 (125822,377319,251494) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=69, convex hull=33) After retessellation of defect 21, euler #=-2 (125828,377348,251518) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=60, convex hull=70) After retessellation of defect 22, euler #=-1 (125847,377437,251589) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=29, convex hull=75) After retessellation of defect 23, euler #=0 (125863,377517,251654) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=106, convex hull=107) After retessellation of defect 24, euler #=1 (125900,377674,251775) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=17, convex hull=52) After retessellation of defect 25, euler #=2 (125909,377721,251814) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.12-->6.94) (max @ vno 106198 --> 106201) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.12-->6.94) (max @ vno 106198 --> 106201) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 88 mutations (34.8%), 165 crossovers (65.2%), 58 vertices were eliminated building final representation... 841 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125909, nf=251814, ne=377721, g=0) writing corrected surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 14.0 minutes 0 defective edges removing intersecting faces 000: 111 intersecting 001: 10 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 125909 - 377721 + 251814 = 2 --> 0 holes F =2V-4: 251814 = 251818-4 (0) 2E=3F: 755442 = 755442 (0) total defect index = 0 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat May 21 19:26:18 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs good_output rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11199 bright wm thresholded. 3542 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig... computing class statistics... border white: 234602 voxels (1.40%) border gray 265704 voxels (1.58%) WM (92.0): 92.8 +- 9.0 [70.0 --> 110.0] GM (78.0) : 75.4 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.4 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 37.9 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.04) (max @ vno 25471 --> 25516) face area 0.28 +- 0.12 (0.00-->1.80) mean absolute distance = 0.85 +- 1.06 3113 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=63 using class modes intead of means.... mean inside = 91.6, mean outside = 71.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=74.1, 128 (128) missing vertices, mean dist 0.4 [0.9 (%26.6)->0.8 (%73.4))] %49 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.10-->3.25) (max @ vno 95981 --> 95027) face area 0.28 +- 0.14 (0.00-->1.50) mean absolute distance = 0.40 +- 0.75 2828 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5816684.0, rms=12.40 001: dt: 0.5000, sse=5828585.5, rms=9.18 002: dt: 0.5000, sse=6012461.0, rms=7.12 003: dt: 0.5000, sse=6250080.5, rms=5.73 004: dt: 0.5000, sse=6367354.0, rms=4.83 005: dt: 0.5000, sse=6545091.5, rms=4.28 006: dt: 0.5000, sse=6664019.0, rms=3.99 007: dt: 0.5000, sse=6757811.5, rms=3.81 008: dt: 0.5000, sse=6777065.0, rms=3.73 009: dt: 0.5000, sse=6817743.5, rms=3.65 rms = 3.61, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6791787.5, rms=3.61 011: dt: 0.2500, sse=4110045.5, rms=2.41 012: dt: 0.2500, sse=3712685.8, rms=2.08 013: dt: 0.2500, sse=3527173.5, rms=1.98 014: dt: 0.2500, sse=3472845.8, rms=1.92 rms = 1.90, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3439205.0, rms=1.90 016: dt: 0.1250, sse=3366337.2, rms=1.84 rms = 1.83, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3344813.8, rms=1.83 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=77.7, 113 (58) missing vertices, mean dist -0.3 [0.5 (%71.3)->0.3 (%28.7))] %61 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.10-->3.46) (max @ vno 89580 --> 89581) face area 0.36 +- 0.17 (0.00-->1.89) mean absolute distance = 0.31 +- 0.46 2908 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4034636.8, rms=5.19 018: dt: 0.5000, sse=4330797.0, rms=3.24 rms = 3.40, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3977604.2, rms=2.51 020: dt: 0.2500, sse=3796526.0, rms=1.94 021: dt: 0.2500, sse=3672390.8, rms=1.68 022: dt: 0.2500, sse=3628309.0, rms=1.59 rms = 1.54, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3584581.8, rms=1.54 024: dt: 0.1250, sse=3539070.8, rms=1.49 rms = 1.49, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3515921.5, rms=1.49 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.1, 88 (52) missing vertices, mean dist -0.2 [0.3 (%73.8)->0.2 (%26.2))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.05-->3.88) (max @ vno 90507 --> 91373) face area 0.35 +- 0.16 (0.00-->1.95) mean absolute distance = 0.24 +- 0.35 2787 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3901079.5, rms=4.37 026: dt: 0.5000, sse=4108321.8, rms=2.97 rms = 3.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3804114.8, rms=2.02 028: dt: 0.2500, sse=3703718.5, rms=1.55 029: dt: 0.2500, sse=3679003.5, rms=1.38 rms = 1.37, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3662768.0, rms=1.37 031: dt: 0.1250, sse=3608986.5, rms=1.31 rms = 1.32, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3608986.5, rms=1.31 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.5, 85 (44) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3659870.5, rms=2.11 rms = 2.24, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3727087.0, rms=1.43 034: dt: 0.2500, sse=3899093.0, rms=1.00 rms = 1.03, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3897072.8, rms=0.99 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group generating cortex label... 15 non-cortical segments detected only using segment with 1819 vertices erasing segment 1 (vno[0] = 47729) erasing segment 2 (vno[0] = 74906) erasing segment 3 (vno[0] = 79637) erasing segment 4 (vno[0] = 82633) erasing segment 5 (vno[0] = 83616) erasing segment 6 (vno[0] = 84537) erasing segment 7 (vno[0] = 87567) erasing segment 8 (vno[0] = 88549) erasing segment 9 (vno[0] = 88713) erasing segment 10 (vno[0] = 95870) erasing segment 11 (vno[0] = 95892) erasing segment 12 (vno[0] = 96760) erasing segment 13 (vno[0] = 97476) erasing segment 14 (vno[0] = 98881) writing cortex label to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.cortex.label... LabelWrite: saving to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.cortex.label writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.area vertex spacing 0.90 +- 0.26 (0.07-->3.96) (max @ vno 90507 --> 91373) face area 0.34 +- 0.16 (0.00-->1.94) refinement took 5.9 minutes #-------------------------------------------- #@# Smooth2 rh Sat May 21 19:32:16 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Sat May 21 19:32:20 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.9 mm, total surface area = 78376 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 278 vertices thresholded to be in k1 ~ [-0.24 0.40], k2 ~ [-0.08 0.07] total integrated curvature = 0.594*4pi (7.460) --> 0 handles ICI = 1.5, FI = 9.4, variation=159.391 158 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 135 vertices thresholded to be in [-0.12 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.023 done. #-------------------------------------------- #@# Sphere rh Sat May 21 19:34:27 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.15 hours scaling brain by 0.292... pass 1: epoch 1 of 3 starting distance error %18.95 pass 1: epoch 2 of 3 starting distance error %18.93 unfolding complete - removing small folds... starting distance error %18.80 removing remaining folds... final distance error %18.81 #-------------------------------------------- #@# Surf Reg rh Sat May 21 20:43:16 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_register -curv ../surf/rh.sphere /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.590 curvature mean = 0.050, std = 0.939 curvature mean = 0.018, std = 0.872 curvature mean = 0.029, std = 0.962 curvature mean = 0.008, std = 0.948 curvature mean = 0.023, std = 0.972 curvature mean = 0.003, std = 0.978 curvature mean = 0.021, std = 0.973 curvature mean = 0.001, std = 0.991 curvature mean = -0.024, std = 0.277 curvature mean = 0.006, std = 0.071 curvature mean = 0.058, std = 0.370 curvature mean = 0.005, std = 0.085 curvature mean = 0.027, std = 0.564 curvature mean = 0.005, std = 0.092 curvature mean = 0.014, std = 0.700 curvature mean = 0.006, std = 0.095 curvature mean = 0.004, std = 0.805 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sat May 21 21:18:04 EDT 2011 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Sat May 21 21:18:06 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mrisp_paint -a 5 /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Sat May 21 21:18:09 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1056 labels changed using aseg relabeling using gibbs priors... 000: 2884 changed, 125909 examined... 001: 627 changed, 12212 examined... 002: 163 changed, 3490 examined... 003: 60 changed, 960 examined... 004: 13 changed, 356 examined... 005: 8 changed, 85 examined... 006: 2 changed, 45 examined... 007: 0 changed, 15 examined... 182 labels changed using aseg 000: 101 total segments, 64 labels (329 vertices) changed 001: 39 total segments, 2 labels (11 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1659 vertices marked for relabeling... 1659 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 49 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sat May 21 21:18:58 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs good_output rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/brain.finalsurfs.mgz... reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... 11199 bright wm thresholded. 3542 bright non-wm voxels segmented. reading original surface position from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig... computing class statistics... border white: 234602 voxels (1.40%) border gray 265704 voxels (1.58%) WM (92.0): 92.8 +- 9.0 [70.0 --> 110.0] GM (78.0) : 75.4 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.4 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 37.9 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.3 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=63 using class modes intead of means.... mean inside = 91.6, mean outside = 71.6 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.04) (max @ vno 25471 --> 25516) face area 0.28 +- 0.12 (0.00-->1.80) mean absolute distance = 0.85 +- 1.07 3195 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 416 points - only 0.00% unknown deleting segment 2 with 22 points - only 0.00% unknown mean border=74.1, 128 (128) missing vertices, mean dist 0.4 [0.9 (%26.6)->0.8 (%73.4))] %49 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.10-->3.25) (max @ vno 95981 --> 95027) face area 0.28 +- 0.14 (0.00-->1.52) mean absolute distance = 0.40 +- 0.75 2862 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5828176.0, rms=12.39 001: dt: 0.5000, sse=5839678.0, rms=9.17 002: dt: 0.5000, sse=6027195.0, rms=7.12 003: dt: 0.5000, sse=6268258.5, rms=5.72 004: dt: 0.5000, sse=6389153.5, rms=4.82 005: dt: 0.5000, sse=6565399.0, rms=4.28 006: dt: 0.5000, sse=6690848.0, rms=3.98 007: dt: 0.5000, sse=6784797.5, rms=3.81 008: dt: 0.5000, sse=6804822.5, rms=3.72 009: dt: 0.5000, sse=6843070.0, rms=3.65 rms = 3.61, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=6820600.0, rms=3.61 011: dt: 0.2500, sse=4126014.8, rms=2.41 012: dt: 0.2500, sse=3728254.8, rms=2.07 013: dt: 0.2500, sse=3542564.5, rms=1.98 014: dt: 0.2500, sse=3488026.2, rms=1.92 rms = 1.90, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=3454284.8, rms=1.90 016: dt: 0.1250, sse=3381478.8, rms=1.84 rms = 1.83, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3359932.5, rms=1.83 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 3 with 366 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown mean border=77.7, 113 (58) missing vertices, mean dist -0.3 [0.5 (%71.2)->0.3 (%28.8))] %61 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.10-->3.42) (max @ vno 89580 --> 89581) face area 0.36 +- 0.17 (0.00-->1.89) mean absolute distance = 0.31 +- 0.46 2986 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4049214.2, rms=5.18 018: dt: 0.5000, sse=4350739.5, rms=3.23 rms = 3.39, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3993672.2, rms=2.51 020: dt: 0.2500, sse=3811283.5, rms=1.94 021: dt: 0.2500, sse=3687590.8, rms=1.68 022: dt: 0.2500, sse=3641618.8, rms=1.59 rms = 1.54, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3598179.0, rms=1.54 rms = 1.49, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3552938.0, rms=1.49 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 358 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 6 points - only 33.33% unknown mean border=81.1, 64 (27) missing vertices, mean dist -0.2 [0.3 (%73.8)->0.2 (%26.2))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.04-->3.86) (max @ vno 90507 --> 91373) face area 0.35 +- 0.16 (0.00-->2.45) mean absolute distance = 0.24 +- 0.35 2841 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3939336.8, rms=4.38 025: dt: 0.5000, sse=4130331.5, rms=2.97 rms = 3.29, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3822036.0, rms=2.02 027: dt: 0.2500, sse=3718598.8, rms=1.56 028: dt: 0.2500, sse=3693714.2, rms=1.38 rms = 1.38, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3674178.5, rms=1.38 030: dt: 0.1250, sse=3620533.5, rms=1.31 rms = 1.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3620533.5, rms=1.31 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 382 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 28 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown mean border=82.5, 61 (22) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3672715.5, rms=2.11 rms = 2.24, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3738802.5, rms=1.43 033: dt: 0.2500, sse=3906695.5, rms=1.00 rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=3904924.8, rms=0.99 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=53.0, 78 (78) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.1 (%100.0))] %23 local maxima, %62 large gradients and %10 min vals, 881 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=22660790.0, rms=29.11 001: dt: 0.5000, sse=16764797.0, rms=24.51 002: dt: 0.5000, sse=12481235.0, rms=20.55 003: dt: 0.5000, sse=9611524.0, rms=17.31 004: dt: 0.5000, sse=8086235.0, rms=14.64 005: dt: 0.5000, sse=7125258.5, rms=12.41 006: dt: 0.5000, sse=6549590.5, rms=10.59 007: dt: 0.5000, sse=6110220.5, rms=9.03 008: dt: 0.5000, sse=5899991.0, rms=7.67 009: dt: 0.5000, sse=5760583.0, rms=6.51 010: dt: 0.5000, sse=5765572.0, rms=5.57 011: dt: 0.5000, sse=5768802.0, rms=4.89 012: dt: 0.5000, sse=5898504.0, rms=4.44 013: dt: 0.5000, sse=5941561.5, rms=4.17 014: dt: 0.5000, sse=6027329.0, rms=4.00 015: dt: 0.5000, sse=6029091.0, rms=3.90 016: dt: 0.5000, sse=6085764.5, rms=3.83 017: dt: 0.5000, sse=6097597.0, rms=3.78 rms = 3.75, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=6141603.0, rms=3.75 019: dt: 0.2500, sse=4048269.0, rms=2.87 020: dt: 0.2500, sse=3810696.2, rms=2.65 rms = 2.61, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3693253.0, rms=2.61 022: dt: 0.1250, sse=3561975.0, rms=2.51 rms = 2.50, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3542088.0, rms=2.50 positioning took 2.3 minutes mean border=49.7, 347 (14) missing vertices, mean dist 0.2 [0.2 (%44.0)->0.6 (%56.0))] %49 local maxima, %40 large gradients and % 6 min vals, 214 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4401104.5, rms=5.82 024: dt: 0.5000, sse=4444246.0, rms=4.22 025: dt: 0.5000, sse=5525016.5, rms=3.93 rms = 3.92, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=5830169.0, rms=3.92 027: dt: 0.2500, sse=4413906.5, rms=2.92 028: dt: 0.2500, sse=4241587.0, rms=2.63 029: dt: 0.2500, sse=4134661.5, rms=2.58 rms = 2.53, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4130765.0, rms=2.53 031: dt: 0.1250, sse=4001754.5, rms=2.43 rms = 2.41, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3984009.0, rms=2.41 positioning took 0.8 minutes mean border=46.9, 418 (9) missing vertices, mean dist 0.2 [0.2 (%37.6)->0.4 (%62.4))] %65 local maxima, %23 large gradients and % 6 min vals, 273 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4306586.0, rms=4.24 033: dt: 0.5000, sse=4394155.5, rms=3.66 rms = 3.71, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4121928.2, rms=2.83 035: dt: 0.2500, sse=4209532.5, rms=2.47 036: dt: 0.2500, sse=4194436.5, rms=2.38 rms = 2.35, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4198204.5, rms=2.35 038: dt: 0.1250, sse=4095301.2, rms=2.24 rms = 2.23, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4084662.2, rms=2.23 positioning took 0.7 minutes mean border=45.5, 879 (9) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))] %73 local maxima, %16 large gradients and % 5 min vals, 220 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4156084.5, rms=2.82 rms = 3.32, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4039474.8, rms=2.40 041: dt: 0.2500, sse=4102634.5, rms=2.23 042: dt: 0.2500, sse=4162210.8, rms=2.17 rms = 2.14, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=4217633.5, rms=2.14 044: dt: 0.1250, sse=4132882.5, rms=2.07 rms = 2.06, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4132574.5, rms=2.06 positioning took 0.6 minutes writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.area.pial vertex spacing 1.02 +- 0.41 (0.05-->7.65) (max @ vno 87580 --> 87564) face area 0.41 +- 0.29 (0.00-->6.78) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 125909 vertices processed 25000 of 125909 vertices processed 50000 of 125909 vertices processed 75000 of 125909 vertices processed 100000 of 125909 vertices processed 125000 of 125909 vertices processed 0 of 125909 vertices processed 25000 of 125909 vertices processed 50000 of 125909 vertices processed 75000 of 125909 vertices processed 100000 of 125909 vertices processed 125000 of 125909 vertices processed thickness calculation complete, 306:577 truncations. 61083 vertices at 0 distance 80820 vertices at 1 distance 63424 vertices at 2 distance 22355 vertices at 3 distance 6804 vertices at 4 distance 2273 vertices at 5 distance 971 vertices at 6 distance 454 vertices at 7 distance 258 vertices at 8 distance 150 vertices at 9 distance 83 vertices at 10 distance 49 vertices at 11 distance 38 vertices at 12 distance 31 vertices at 13 distance 23 vertices at 14 distance 26 vertices at 15 distance 9 vertices at 16 distance 8 vertices at 17 distance 4 vertices at 18 distance 7 vertices at 19 distance 2 vertices at 20 distance writing curvature file /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.thickness positioning took 11.1 minutes #-------------------------------------------- #@# Surf Volume rh Sat May 21 21:30:05 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Sat May 21 21:30:06 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab good_output rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1319 901 2439 2.632 0.538 0.124 0.036 13 1.9 bankssts 947 656 1797 2.548 0.563 0.163 0.058 27 2.5 caudalanteriorcingulate 2962 2067 5752 2.486 0.505 0.131 0.039 32 5.0 caudalmiddlefrontal 1961 1278 2525 1.762 0.457 0.173 0.074 45 5.8 cuneus 502 356 1606 3.020 0.847 0.139 0.033 6 0.7 entorhinal 4740 3319 8586 2.244 0.688 0.144 0.043 70 8.6 fusiform 7869 5503 14660 2.366 0.604 0.151 0.056 131 16.9 inferiorparietal 4188 2879 8747 2.483 0.746 0.144 0.051 68 9.2 inferiortemporal 1304 830 2067 2.377 0.849 0.154 0.056 32 3.0 isthmuscingulate 6430 4391 10209 2.072 0.533 0.160 0.059 113 15.1 lateraloccipital 3689 2514 6397 2.279 0.705 0.147 0.064 63 8.5 lateralorbitofrontal 3674 2590 4950 1.754 0.501 0.150 0.048 53 7.4 lingual 3002 2103 5485 2.231 0.676 0.154 0.090 85 7.8 medialorbitofrontal 5112 3584 11336 2.620 0.650 0.147 0.072 177 18.2 middletemporal 1081 718 2068 2.322 0.911 0.103 0.035 9 1.5 parahippocampal 2484 1620 3722 2.114 0.542 0.119 0.047 26 5.9 paracentral 2240 1532 4289 2.492 0.475 0.135 0.042 29 3.7 parsopercularis 1089 722 2245 2.509 0.483 0.158 0.063 20 2.9 parsorbitalis 1816 1258 3638 2.505 0.507 0.146 0.061 27 3.8 parstriangularis 1634 1094 1663 1.537 0.355 0.133 0.042 15 2.9 pericalcarine 5220 3483 7361 1.866 0.610 0.125 0.043 64 10.1 postcentral 1632 1140 3157 2.450 0.591 0.160 0.068 48 3.9 posteriorcingulate 6890 4414 12105 2.499 0.570 0.119 0.038 69 10.8 precentral 5787 3908 9460 2.212 0.637 0.152 0.061 108 14.9 precuneus 710 476 1492 2.694 0.676 0.134 0.050 12 1.5 rostralanteriorcingulate 7126 4994 13430 2.285 0.595 0.152 0.062 124 19.8 rostralmiddlefrontal 8598 5942 17075 2.473 0.578 0.146 0.057 132 19.7 superiorfrontal 7515 4998 11269 2.035 0.522 0.132 0.043 93 13.4 superiorparietal 5213 3561 10120 2.506 0.656 0.130 0.045 68 9.6 superiortemporal 5603 3755 9967 2.359 0.573 0.136 0.049 76 10.6 supramarginal 311 209 820 2.685 0.585 0.194 0.075 10 1.0 frontalpole 509 390 2046 3.601 0.460 0.163 0.070 8 1.6 temporalpole 593 351 803 2.055 0.351 0.139 0.116 12 4.3 transversetemporal 3623 2355 7085 2.823 0.882 0.130 0.080 126 11.8 insula #----------------------------------------- #@# Cortical Parc 2 rh Sat May 21 21:30:20 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 good_output rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0_x86_64/stable5/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /space/freesurfer/centos4.0_x86_64/stable5/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 44 labels changed using aseg relabeling using gibbs priors... 000: 9168 changed, 125909 examined... 001: 2069 changed, 35068 examined... 002: 666 changed, 10634 examined... 003: 306 changed, 3666 examined... 004: 136 changed, 1698 examined... 005: 64 changed, 758 examined... 006: 44 changed, 365 examined... 007: 21 changed, 228 examined... 008: 14 changed, 122 examined... 009: 16 changed, 86 examined... 010: 5 changed, 81 examined... 011: 6 changed, 34 examined... 012: 5 changed, 32 examined... 013: 5 changed, 26 examined... 014: 4 changed, 23 examined... 015: 0 changed, 15 examined... 25 labels changed using aseg 000: 246 total segments, 167 labels (2070 vertices) changed 001: 93 total segments, 14 labels (35 vertices) changed 002: 80 total segments, 1 labels (1 vertices) changed 003: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 126 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1112 vertices marked for relabeling... 1112 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 59 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sat May 21 21:31:19 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab good_output rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 652 461 1185 2.180 0.577 0.161 0.050 12 1.4 G_and_S_frontomargin 1476 1024 2924 2.449 0.615 0.165 0.056 28 3.4 G_and_S_occipital_inf 1537 997 2453 2.052 0.555 0.131 0.044 18 2.9 G_and_S_paracentral 1110 749 2293 2.533 0.581 0.141 0.043 14 2.0 G_and_S_subcentral 987 684 1859 2.141 0.603 0.159 0.061 22 2.3 G_and_S_transv_frontopol 2481 1699 4585 2.433 0.577 0.132 0.046 35 4.6 G_and_S_cingul-Ant 1305 917 2426 2.346 0.542 0.147 0.048 21 2.7 G_and_S_cingul-Mid-Ant 1238 854 2208 2.334 0.558 0.132 0.057 31 2.1 G_and_S_cingul-Mid-Post 561 372 1373 2.836 0.448 0.198 0.072 16 1.9 G_cingul-Post-dorsal 250 166 508 2.669 0.862 0.150 0.074 4 0.6 G_cingul-Post-ventral 1912 1233 2515 1.762 0.442 0.176 0.078 47 6.1 G_cuneus 1193 797 2772 2.669 0.476 0.155 0.054 23 2.7 G_front_inf-Opercular 228 151 565 2.783 0.336 0.175 0.087 6 0.9 G_front_inf-Orbital 926 652 2346 2.712 0.449 0.155 0.079 18 2.3 G_front_inf-Triangul 3669 2604 8401 2.516 0.580 0.159 0.061 68 9.9 G_front_middle 5905 4018 13292 2.623 0.567 0.165 0.075 120 18.9 G_front_sup 456 318 1074 2.991 0.846 0.119 0.045 6 0.6 G_Ins_lg_and_S_cent_ins 545 342 1734 3.520 0.696 0.180 0.104 25 2.8 G_insular_short 1894 1320 3969 2.422 0.521 0.174 0.068 40 5.2 G_occipital_middle 1585 1049 2496 2.079 0.601 0.149 0.056 25 3.8 G_occipital_sup 1961 1354 4160 2.503 0.548 0.150 0.052 37 4.1 G_oc-temp_lat-fusifor 2256 1561 3298 1.806 0.555 0.155 0.055 35 5.0 G_oc-temp_med-Lingual 1771 1183 4430 2.897 0.931 0.135 0.057 26 4.1 G_oc-temp_med-Parahip 2724 1853 5948 2.480 0.705 0.169 0.080 63 8.0 G_orbital 2919 2049 6861 2.656 0.579 0.179 0.075 69 8.1 G_pariet_inf-Angular 3063 2041 6323 2.531 0.549 0.152 0.062 57 7.4 G_pariet_inf-Supramar 2153 1454 4017 2.219 0.486 0.143 0.048 35 4.1 G_parietal_sup 1968 1283 3050 1.942 0.524 0.135 0.059 35 5.6 G_postcentral 2572 1589 5633 2.738 0.472 0.132 0.049 33 5.1 G_precentral 2908 1936 5686 2.398 0.609 0.167 0.079 75 9.5 G_precuneus 880 652 2062 2.502 0.505 0.210 0.118 31 3.8 G_rectus 376 245 643 2.617 0.642 0.203 0.519 100 5.3 G_subcallosal 452 262 726 2.251 0.411 0.146 0.151 13 4.3 G_temp_sup-G_T_transv 1805 1240 4563 2.798 0.645 0.156 0.062 35 4.2 G_temp_sup-Lateral 792 548 1610 2.598 0.764 0.092 0.024 4 0.8 G_temp_sup-Plan_polar 814 550 1438 2.318 0.500 0.119 0.047 9 1.4 G_temp_sup-Plan_tempo 2570 1806 6341 2.636 0.733 0.169 0.066 59 7.4 G_temporal_inf 3153 2258 8153 2.765 0.628 0.169 0.099 161 15.9 G_temporal_middle 396 261 551 2.316 0.443 0.115 0.024 3 0.4 Lat_Fis-ant-Horizont 164 118 303 2.418 0.621 0.141 0.040 1 0.2 Lat_Fis-ant-Vertical 1503 1000 2017 2.313 0.527 0.111 0.027 10 1.6 Lat_Fis-post 2948 2005 4432 1.871 0.476 0.172 0.066 56 8.0 Pole_occipital 1679 1162 4880 3.000 0.746 0.157 0.056 29 4.3 Pole_temporal 1579 1077 1825 1.875 0.730 0.130 0.036 14 2.2 S_calcarine 3029 2005 3526 1.923 0.708 0.107 0.029 23 3.7 S_central 1392 968 1883 2.024 0.527 0.106 0.026 8 1.6 S_cingul-Marginalis 750 492 1216 2.583 0.792 0.112 0.032 5 1.0 S_circular_insula_ant 1160 730 1575 2.320 0.778 0.081 0.022 4 0.9 S_circular_insula_inf 1343 906 1976 2.340 0.464 0.115 0.030 9 1.7 S_circular_insula_sup 941 651 1147 1.766 0.609 0.109 0.023 6 0.9 S_collat_transv_ant 667 439 702 1.792 0.365 0.134 0.042 7 1.2 S_collat_transv_post 2187 1481 3420 2.277 0.433 0.130 0.042 25 3.4 S_front_inf 1368 979 2585 2.285 0.626 0.140 0.083 21 5.8 S_front_middle 2262 1590 3423 2.183 0.503 0.117 0.032 18 3.0 S_front_sup 861 573 1147 2.061 0.451 0.116 0.034 6 1.2 S_interm_prim-Jensen 3278 2201 3988 1.902 0.447 0.117 0.031 26 4.3 S_intrapariet_and_P_trans 858 583 1054 1.826 0.349 0.136 0.038 10 1.4 S_oc_middle_and_Lunatus 1558 1056 1843 1.859 0.399 0.113 0.030 11 1.9 S_oc_sup_and_transversal 545 376 748 2.254 0.405 0.124 0.033 4 0.7 S_occipital_ant 788 545 1018 2.075 0.579 0.132 0.039 8 1.2 S_oc-temp_lat 1981 1439 2397 1.690 0.515 0.116 0.025 16 2.1 S_oc-temp_med_and_Lingual 499 345 665 2.013 0.492 0.123 0.032 4 0.7 S_orbital_lateral 979 682 1259 1.817 0.636 0.105 0.025 6 1.0 S_orbital_med-olfact 1243 851 1987 2.330 0.606 0.141 0.053 18 2.7 S_orbital-H_Shaped 2165 1445 2494 1.877 0.564 0.144 0.053 30 5.0 S_parieto_occipital 1346 838 1482 2.244 0.794 0.157 0.055 45 3.1 S_pericallosal 1641 1105 1896 1.811 0.521 0.110 0.027 11 1.9 S_postcentral 1643 1116 2416 2.279 0.391 0.111 0.030 12 1.9 S_precentral-inf-part 974 674 1375 2.340 0.474 0.116 0.029 6 1.2 S_precentral-sup-part 463 309 525 1.746 0.683 0.110 0.024 3 0.5 S_suborbital 948 658 1489 2.089 0.466 0.135 0.039 11 1.5 S_subparietal 1154 777 1634 2.433 0.527 0.125 0.034 9 1.7 S_temporal_inf 5771 3982 9227 2.340 0.578 0.120 0.036 61 8.2 S_temporal_sup 263 203 347 1.917 0.474 0.155 0.034 3 0.4 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Sat May 21 21:31:36 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon good_output SUBJECTS_DIR is /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 8 writing volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sat May 21 21:45:38 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /space/freesurfer/centos4.0_x86_64/stable5/ASegStatsLUT.txt --subject good_output $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /space/freesurfer/centos4.0_x86_64/stable5/ASegStatsLUT.txt --subject good_output sysname Linux hostname compute-0-1.local machine x86_64 user khoa atlas_icv (eTIV) = 1513067 mm^3 (det: 1.287521 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 219240 rh white matter volume 223721 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 251695.722590, pTot = 457481.126381 c = 205785.403791 rh surface-based volumes (mm3): wTot = 257051.359334, pTot = 461543.747231 c = 204492.387897 Computing SupraTentVolCor SupraTentVolCor = 62566.000 SupraTentVol = 981590.874 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 16972 16972 4 5 Left-Inf-Lat-Vent 960 960 5 7 Left-Cerebellum-White-Matter 11231 11231 6 8 Left-Cerebellum-Cortex 41845 41845 7 10 Left-Thalamus-Proper 6172 6172 8 11 Left-Caudate 5300 5300 9 12 Left-Putamen 5516 5516 10 13 Left-Pallidum 1640 1640 11 14 3rd-Ventricle 1569 1569 12 15 4th-Ventricle 2001 2001 13 16 Brain-Stem 17538 17538 14 17 Left-Hippocampus 3997 3997 15 18 Left-Amygdala 1402 1402 16 24 CSF 1126 1126 17 26 Left-Accumbens-area 572 572 18 28 Left-VentralDC 3117 3117 19 30 Left-vessel 119 119 20 31 Left-choroid-plexus 1982 1982 23 43 Right-Lateral-Ventricle 20010 20010 24 44 Right-Inf-Lat-Vent 957 957 25 46 Right-Cerebellum-White-Matter 11150 11150 26 47 Right-Cerebellum-Cortex 41935 41935 27 49 Right-Thalamus-Proper 6074 6074 28 50 Right-Caudate 4887 4887 29 51 Right-Putamen 5265 5265 30 52 Right-Pallidum 1482 1482 31 53 Right-Hippocampus 4139 4139 32 54 Right-Amygdala 1446 1446 33 58 Right-Accumbens-area 707 707 34 60 Right-VentralDC 3288 3288 35 62 Right-vessel 113 113 36 63 Right-choroid-plexus 2230 2230 37 72 5th-Ventricle 49 49 38 77 WM-hypointensities 4318 4318 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 85 85 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 308 308 45 251 CC_Posterior 957 957 46 252 CC_Mid_Posterior 267 267 47 253 CC_Central 348 348 48 254 CC_Mid_Anterior 335 335 49 255 CC_Anterior 723 723 Reporting on 45 segmentations SubCortGrayVol = 156322 #----------------------------------------- #@# AParc-to-ASeg Sat May 21 21:55:34 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_aparc2aseg --s good_output --volmask SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output outvol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 403810 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_aparc2aseg --s good_output --volmask --a2009s SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output outvol /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 403810 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Sat May 21 21:58:09 EDT 2011 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_aparc2aseg --s good_output --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs subject good_output outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz Reading lh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading lh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial Loading lh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading rh pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial Loading rh annotations from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/ribbon.mgz Loading filled from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8576 vertices from left hemi Ripped 8536 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aseg.mgz Loading Ctx Seg File /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 822455 Used brute-force search on 178 voxels Fixing Parahip LH WM Found 23 clusters 0 k 2.000000 1 k 15.000000 2 k 1.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1450.000000 8 k 1.000000 9 k 3.000000 10 k 6.000000 11 k 2.000000 12 k 1.000000 13 k 1.000000 14 k 1.000000 15 k 5.000000 16 k 1.000000 17 k 5.000000 18 k 1.000000 19 k 1.000000 20 k 1.000000 21 k 4.000000 22 k 5.000000 Fixing Parahip RH WM Found 13 clusters 0 k 1.000000 1 k 1.000000 2 k 1575.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 2.000000 9 k 1.000000 10 k 42.000000 11 k 1.000000 12 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject good_output --surf-wm-vol --ctab /space/freesurfer/centos4.0_x86_64/stable5/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject good_output --surf-wm-vol --ctab /space/freesurfer/centos4.0_x86_64/stable5/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-1.local machine x86_64 user khoa atlas_icv (eTIV) = 1513067 mm^3 (det: 1.287521 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 219240 rh white matter volume 223721 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1529037 # brainmaskvolume 1529037.0 # nbrainsegvoxels 227503 # brainsegvolume 227503.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 3694 3694 2 3002 wm-lh-caudalanteriorcingulate 2828 2828 3 3003 wm-lh-caudalmiddlefrontal 6133 6133 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 1720 1720 6 3006 wm-lh-entorhinal 652 652 7 3007 wm-lh-fusiform 6604 6604 8 3008 wm-lh-inferiorparietal 9648 9648 9 3009 wm-lh-inferiortemporal 6333 6333 10 3010 wm-lh-isthmuscingulate 3837 3837 11 3011 wm-lh-lateraloccipital 6719 6719 12 3012 wm-lh-lateralorbitofrontal 5491 5491 13 3013 wm-lh-lingual 4593 4593 14 3014 wm-lh-medialorbitofrontal 4307 4307 15 3015 wm-lh-middletemporal 5587 5587 16 3016 wm-lh-parahippocampal 1601 1601 17 3017 wm-lh-paracentral 3383 3383 18 3018 wm-lh-parsopercularis 3044 3044 19 3019 wm-lh-parsorbitalis 953 953 20 3020 wm-lh-parstriangularis 2580 2580 21 3021 wm-lh-pericalcarine 1922 1922 22 3022 wm-lh-postcentral 7683 7683 23 3023 wm-lh-posteriorcingulate 4353 4353 24 3024 wm-lh-precentral 12003 12003 25 3025 wm-lh-precuneus 8585 8585 26 3026 wm-lh-rostralanteriorcingulate 2254 2254 27 3027 wm-lh-rostralmiddlefrontal 10652 10652 28 3028 wm-lh-superiorfrontal 15805 15805 29 3029 wm-lh-superiorparietal 11710 11710 30 3030 wm-lh-superiortemporal 7366 7366 31 3031 wm-lh-supramarginal 9086 9086 32 3032 wm-lh-frontalpole 212 212 33 3033 wm-lh-temporalpole 742 742 34 3034 wm-lh-transversetemporal 804 804 35 3035 wm-lh-insula 9662 9662 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2715 2715 120 4002 wm-rh-caudalanteriorcingulate 2496 2496 121 4003 wm-rh-caudalmiddlefrontal 6116 6116 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1892 1892 124 4006 wm-rh-entorhinal 740 740 125 4007 wm-rh-fusiform 6870 6870 126 4008 wm-rh-inferiorparietal 12221 12221 127 4009 wm-rh-inferiortemporal 4981 4981 128 4010 wm-rh-isthmuscingulate 3468 3468 129 4011 wm-rh-lateraloccipital 8390 8390 130 4012 wm-rh-lateralorbitofrontal 6015 6015 131 4013 wm-rh-lingual 4162 4162 132 4014 wm-rh-medialorbitofrontal 3568 3568 133 4015 wm-rh-middletemporal 6555 6555 134 4016 wm-rh-parahippocampal 1701 1701 135 4017 wm-rh-paracentral 4947 4947 136 4018 wm-rh-parsopercularis 3692 3692 137 4019 wm-rh-parsorbitalis 1036 1036 138 4020 wm-rh-parstriangularis 2673 2673 139 4021 wm-rh-pericalcarine 2081 2081 140 4022 wm-rh-postcentral 6415 6415 141 4023 wm-rh-posteriorcingulate 3915 3915 142 4024 wm-rh-precentral 12500 12500 143 4025 wm-rh-precuneus 9470 9470 144 4026 wm-rh-rostralanteriorcingulate 1880 1880 145 4027 wm-rh-rostralmiddlefrontal 10938 10938 146 4028 wm-rh-superiorfrontal 15254 15254 147 4029 wm-rh-superiorparietal 11641 11641 148 4030 wm-rh-superiortemporal 6703 6703 149 4031 wm-rh-supramarginal 9160 9160 150 4032 wm-rh-frontalpole 209 209 151 4033 wm-rh-temporalpole 578 578 152 4034 wm-rh-transversetemporal 622 622 153 4035 wm-rh-insula 8997 8997 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 25027 25027 237 5002 Right-UnsegmentedWhiteMatter 26103 26103 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label #-------------------------------------------- #@# BA Labels lh Sat May 21 22:15:57 EDT 2011 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA1.label --trgsubject good_output --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./lh.BA1.label 4503 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA2.label --trgsubject good_output --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 918 Checking for and removing duplicates Writing label file ./lh.BA2.label 8827 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3a.label --trgsubject good_output --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4207 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3b.label --trgsubject good_output --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 453 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6436 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4a.label --trgsubject good_output --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 252 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6036 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4p.label --trgsubject good_output --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 187 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4257 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA6.label --trgsubject good_output --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 643 Checking for and removing duplicates Writing label file ./lh.BA6.label 14232 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA44.label --trgsubject good_output --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 370 Checking for and removing duplicates Writing label file ./lh.BA44.label 4551 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA45.label --trgsubject good_output --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 508 Checking for and removing duplicates Writing label file ./lh.BA45.label 3930 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V1.label --trgsubject good_output --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 518 Checking for and removing duplicates Writing label file ./lh.V1.label 5159 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V2.label --trgsubject good_output --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 1853 Checking for and removing duplicates Writing label file ./lh.V2.label 9967 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.MT.label --trgsubject good_output --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = good_output trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./lh.MT.label 2227 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s good_output --hemi lh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose Reading ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label cmdline mris_label2annot --s good_output --hemi lh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user khoa subject good_output hemi lh SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs ColorTable /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 88667 unhit vertices Writing annot to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab good_output lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1117 689 1709 2.033 0.467 0.154 0.178 24 3.9 BA1 4324 2884 6652 2.170 0.511 0.139 0.057 86 12.4 BA2 908 623 856 1.733 0.346 0.128 0.035 8 1.3 BA3a 2625 1796 3760 1.820 0.565 0.129 0.043 31 4.7 BA3b 1557 974 2713 2.473 0.491 0.121 0.673 23 3.5 BA4a 1303 811 1934 2.464 0.515 0.108 0.076 54 6.0 BA4p 7487 5135 16026 2.657 0.557 0.139 0.056 108 16.9 BA6 2411 1650 4277 2.357 0.444 0.135 0.044 30 4.4 BA44 2690 1913 5115 2.267 0.472 0.160 0.062 50 6.7 BA45 2347 1640 2672 1.550 0.420 0.151 0.058 36 5.8 V1 6978 4781 9878 1.870 0.569 0.157 0.055 111 14.5 V2 1571 1075 2507 2.201 0.459 0.139 0.045 20 3.0 MT #-------------------------------------------- #@# BA Labels rh Sat May 21 22:18:03 EDT 2011 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA1.label --trgsubject good_output --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA1.label 4072 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA2.label --trgsubject good_output --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./rh.BA2.label 6827 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3a.label --trgsubject good_output --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4132 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3b.label --trgsubject good_output --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 193 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4715 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4a.label --trgsubject good_output --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5995 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4p.label --trgsubject good_output --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4682 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA6.label --trgsubject good_output --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 601 Checking for and removing duplicates Writing label file ./rh.BA6.label 12857 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA44.label --trgsubject good_output --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 846 Checking for and removing duplicates Writing label file ./rh.BA44.label 7758 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA45.label --trgsubject good_output --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 880 Checking for and removing duplicates Writing label file ./rh.BA45.label 6235 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V1.label --trgsubject good_output --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 797 Checking for and removing duplicates Writing label file ./rh.V1.label 5524 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V2.label --trgsubject good_output --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 2109 Checking for and removing duplicates Writing label file ./rh.V2.label 10125 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.MT.label --trgsubject good_output --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = good_output trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs FREESURFER_HOME /space/freesurfer/centos4.0_x86_64/stable5 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white Reading target registration /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./rh.MT.label 2166 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s good_output --hemi rh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose Reading ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label cmdline mris_label2annot --s good_output --hemi rh --ctab /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user khoa subject good_output hemi rh SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs ColorTable /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 90388 unhit vertices Writing annot to /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab good_output rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /space/freesurfer/centos4.0_x86_64/stable5/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 712 420 1302 2.254 0.445 0.164 0.108 24 3.9 BA1 2430 1699 3486 1.916 0.557 0.116 0.030 20 3.0 BA2 1026 696 935 1.583 0.409 0.120 0.031 7 1.3 BA3a 2002 1348 2466 1.612 0.508 0.124 0.038 19 3.2 BA3b 1500 928 2620 2.442 0.616 0.119 0.057 18 4.5 BA4a 1332 822 2132 2.583 0.580 0.104 0.034 14 1.7 BA4p 6774 4504 13797 2.586 0.534 0.141 0.050 91 14.2 BA6 3819 2572 6625 2.402 0.488 0.126 0.037 41 5.7 BA44 4068 2776 8094 2.445 0.492 0.150 0.061 69 9.4 BA45 2863 1947 3561 1.638 0.451 0.154 0.056 44 6.4 V1 7366 4973 10099 1.869 0.506 0.158 0.059 125 17.6 V2 1629 1162 2969 2.258 0.574 0.156 0.054 27 3.5 MT /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Sat May 21 22:20:11 EDT 2011 mris_spherical_average -erode 1 -orig white -t 0.4 -o good_output label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject good_output. processing subject lh.EC_average... reading output surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 835 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label good_output lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/lh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 287 190 1079 3.382 0.472 0.131 0.058 3 0.5 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Sat May 21 22:20:29 EDT 2011 mris_spherical_average -erode 1 -orig white -t 0.4 -o good_output label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject good_output. processing subject rh.EC_average... reading output surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 818 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label good_output rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/mri/wm.mgz... reading input surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... reading input pial surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.pial... reading input white surface /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 308 199 1092 3.318 0.611 0.135 0.050 4 0.9 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s good_output finished without error at Sat May 21 22:20:49 EDT 2011