Tue Apr 20 09:52:14 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun /usr/local/freesurfer/dev/bin/recon-all -subject avg35rerun -i avg35rerun.mgz -all subjid avg35rerun setenv SUBJECTS_DIR /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun 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-20100420 Linux compute-0-38.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 unlimited vmemoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 268288 total used free shared buffers cached Mem: 32962780 23739372 9223408 0 436428 69616 -/+ buffers/cache: 23233328 9729452 Swap: 32764556 144 32764412 ######################################## program versions used $Id: recon-all,v 1.311 2010/04/15 15:34:44 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.9 2009/10/01 17:57:09 mreuter Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:15-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_convert.c,v 1.166 2010/04/15 19:03:33 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:15-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: tkregister2.c,v 1.117 2010/04/09 23:51:25 greve Exp $ User: lzollei Machine: compute-0-38.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_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:17-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:17-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_watershed.cpp,v 1.81 2010/03/30 18:56:23 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:18-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:18-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:18-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:19-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:19-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_ca_normalize.c,v 1.47 2009/07/24 19:51:58 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:19-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_ca_register.c,v 1.70 2010/01/13 17:46:54 rge21 Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:19-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:20-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:20-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:21-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:21-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:22-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:22-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:22-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_inflate.c,v 1.39 2010/03/03 18:10:53 greve Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:23-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:23-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:23-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:23-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:24-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:24-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:25-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:25-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:25-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:25-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_anatomical_stats.c,v 1.67 2010/03/27 23:58:58 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:26-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:26-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:26-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.29 2010/03/05 17:51:11 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:26-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_robust_register.cpp,v 1.29 2010/03/05 17:51:11 mreuter Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18 2010/03/05 18:19:33 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:27-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_robust_template.cpp,v 1.18 2010/03/05 18:19:33 mreuter Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:28-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:28-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:28-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/04/20-13:52:29-GMT BuildTimeStamp: Apr 20 2010 05:08:55 CVS: $Id: mri_segstats.c,v 1.68 2010/04/05 21:01:34 nicks Exp $ User: lzollei Machine: compute-0-38.local Platform: Linux PlatformVersion: 2.6.18-53.1.19.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 ####################################### /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun mri_convert /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig/001.mgz mri_convert /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig/001.mgz $Id: mri_convert.c,v 1.166 2010/04/15 19:03:33 nicks Exp $ reading from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun.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) writing to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 20 09:52:46 EDT 2010 Found 1 runs /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig/001.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/rawavg.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun mri_convert /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/rawavg.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig.mgz --conform mri_convert /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/rawavg.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166 2010/04/15 19:03:33 nicks Exp $ reading from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/transforms/talairach.xfm /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Tue Apr 20 09:52:59 EDT 2010 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri /usr/local/freesurfer/dev/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux compute-0-38.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 Tue Apr 20 09:53:00 EDT 2010 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.7202 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7202/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7202/nu0.mnc -odt float $Id: mri_convert.c,v 1.166 2010/04/15 19:03:33 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.7202/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Apr 20 09:53:05 EDT 2010 nu_correct -clobber ./tmp.mri_nu_correct.mni.7202/nu0.mnc ./tmp.mri_nu_correct.mni.7202/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7202/0/ [lzollei@compute-0-38.local:/autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/] [2010-04-20 09:53:07] running: /usr/local/freesurfer/dev/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.7202/0/ ./tmp.mri_nu_correct.mni.7202/nu0.mnc ./tmp.mri_nu_correct.mni.7202/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 Number of iterations: 19 CV of field change: 0.000988959 [lzollei@compute-0-38.local:/autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/] [2010-04-20 09:53:43] running: /usr/local/freesurfer/dev/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7202/nu0.mnc ./tmp.mri_nu_correct.mni.7202/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Apr 20 09:53:51 EDT 2010 nu_correct -clobber ./tmp.mri_nu_correct.mni.7202/nu1.mnc ./tmp.mri_nu_correct.mni.7202/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.7202/1/ [lzollei@compute-0-38.local:/autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/] [2010-04-20 09:53:53] running: /usr/local/freesurfer/dev/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.7202/1/ ./tmp.mri_nu_correct.mni.7202/nu1.mnc ./tmp.mri_nu_correct.mni.7202/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 Number of iterations: 13 CV of field change: 0.000990828 [lzollei@compute-0-38.local:/autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/] [2010-04-20 09:54:19] running: /usr/local/freesurfer/dev/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7202/nu1.mnc ./tmp.mri_nu_correct.mni.7202/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.7202/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.7202/ones.mgz $Id: mri_binarize.c,v 1.23 2010/04/02 18:37:53 greve Exp $ cwd /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.7202/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.7202/ones.mgz sysname Linux hostname compute-0-38.local machine x86_64 user lzollei input ./tmp.mri_nu_correct.mni.7202/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.7202/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.7202/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7202/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7202/input.mean.dat Loading ./tmp.mri_nu_correct.mni.7202/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 SubCortGrayVol = 0 Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.7202/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7202/ones.mgz --i ./tmp.mri_nu_correct.mni.7202/nu2.mnc --sum ./tmp.mri_nu_correct.mni.7202/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7202/output.mean.dat Loading ./tmp.mri_nu_correct.mni.7202/ones.mgz Loading ./tmp.mri_nu_correct.mni.7202/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 SubCortGrayVol = 0 Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.7202/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.7202/nu2.mnc ./tmp.mri_nu_correct.mni.7202/nu2.mnc mul .91014887551472917326 Saving result to './tmp.mri_nu_correct.mni.7202/nu2.mnc' (type=3) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.7202/nu2.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.7202/nu2.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166 2010/04/15 19:03:33 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.7202/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) 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 INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to nu.mgz... Tue Apr 20 09:55:27 EDT 2010 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Tue Apr 20 09:55:27 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 20 09:56:19 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7707, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/dev/bin/extract_talairach_avi_QA.awk /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/transforms/talairach_avi.log TalAviQA: 0.96822 z-score: -2 #-------------------------------------------- #@# Intensity Normalization Tue Apr 20 09:56:20 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.161 -0.007 -0.112 3.675; -0.016 1.144 0.094 -4.984; 0.141 -0.182 1.241 10.310; 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 10 seconds. MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 white matter peak found at 111 white matter peak found at 109 gm peak at 87 (87), valley at 82 (82) csf peak at 63, setting threshold to 79 white matter peak found at 111 white matter peak found at 109 gm peak at 64 (64), valley at 11 (11) csf peak at 32, setting threshold to 53 #-------------------------------------------- #@# Skull Stripping Tue Apr 20 09:58:31 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/dev/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/dev/average/RB_all_withskull_2008-03-26.gca'... 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=12.0 skull bounding box = (62, 49, 37) --> (195, 170, 217) using (106, 89, 127) as brain centroid... mean wm in atlas = 126, using box (90,74,105) --> (122, 103,149) to find MRI wm before smoothing, mri peak at 198 after smoothing, mri peak at 196, scaling input intensities by 0.643 scaling channel 0 by 0.642857 initial log_p = -10434.6 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-5.4, 15.6, -8.2): log p = -10382.9 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10378.2, old_max_log_p =-10382.9 (thresh=-10372.5) 0.991 0.034 0.126 -22.247; 0.000 0.966 -0.259 48.796; -0.131 0.257 0.958 -20.849; 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=-10372.5, old_max_log_p =-10378.2 (thresh=-10367.9) 1.029 -0.071 0.114 -12.600; 0.089 1.041 -0.158 16.727; -0.091 0.159 0.963 -12.409; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10369.4, old_max_log_p =-10372.5 (thresh=-10362.2) 1.028 -0.071 0.114 -12.438; 0.089 1.042 -0.158 16.605; -0.091 0.159 0.967 -12.826; 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 1.02753 -0.07080 0.11357 -12.43774; 0.08913 1.04243 -0.15804 16.60541; -0.09117 0.15944 0.96688 -12.82583; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02753 -0.07080 0.11357 -12.43774; 0.08913 1.04243 -0.15804 16.60541; -0.09117 0.15944 0.96688 -12.82583; 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: 005: -log(p) = 10369.4 tol 0.000010 Resulting transform: 1.028 -0.071 0.114 -12.438; 0.089 1.042 -0.158 16.605; -0.091 0.159 0.967 -12.826; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10369.4 (old=-10434.6) transform before final EM align: 1.028 -0.071 0.114 -12.438; 0.089 1.042 -0.158 16.605; -0.091 0.159 0.967 -12.826; 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 1.02753 -0.07080 0.11357 -12.43774; 0.08913 1.04243 -0.15804 16.60541; -0.09117 0.15944 0.96688 -12.82583; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02753 -0.07080 0.11357 -12.43774; 0.08913 1.04243 -0.15804 16.60541; -0.09117 0.15944 0.96688 -12.82583; 0.00000 0.00000 0.00000 1.00000; 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: 007: -log(p) = 1146946.1 tol 0.000000 final transform: 1.028 -0.071 0.114 -12.438; 0.089 1.042 -0.158 16.605; -0.091 0.159 0.967 -12.826; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 17 minutes and 19 seconds. mri_watershed -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 Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* 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=97 z=127 r=60 first estimation of the main basin volume: 930777 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=109, y=85, z=98, Imax=255 CSF=11, 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=11623271936 voxels, voxel volume =1.000 = 11623271936 mmm3 = 11623272.448 cm3 done. PostAnalyze...Basin Prior 24 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=128,y=110, z=120, r=9955 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 46116 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2520 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 3114 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 18738 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 18792 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2952 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 3, 32, 63 after analyzing : 3, 22, 32, 32 RIGHT_CER before analyzing : 3, 5, 52, 73 after analyzing : 3, 36, 52, 45 LEFT_CER before analyzing : 3, 4, 46, 73 after analyzing : 3, 32, 46, 42 RIGHT_BRAIN before analyzing : 3, 3, 31, 61 after analyzing : 3, 21, 31, 31 LEFT_BRAIN before analyzing : 3, 3, 32, 63 after analyzing : 3, 22, 32, 32 OTHER before analyzing : 3, 10, 82, 91 after analyzing : 3, 58, 82, 66 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.010 curvature mean = 72.304, std = 7.998 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.13, sigma = 4.98 after rotation: sse = 3.13, sigma = 4.98 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.27, its var is 4.32 before Erosion-Dilatation 0.67% 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 = 1890880 voxels, voxel volume = 1.000 mm3 = 1890880 mmm3 = 1890.880 cm3 ****************************** Saving brainmask.auto.mgz done mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.360000=39.600000 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Apr 20 10:17:14 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca'... 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 = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, 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=29.0 skull bounding box = (64, 51, 39) --> (194, 168, 215) using (107, 90, 127) as brain centroid... mean wm in atlas = 107, using box (91,76,105) --> (122, 104,148) to find MRI wm before smoothing, mri peak at 198 after smoothing, mri peak at 197, scaling input intensities by 0.543 scaling channel 0 by 0.543147 initial log_p = -6369.1 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, 8.5, -16.5): log p = -6071.3 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6071.3, old_max_log_p =-6071.3 (thresh=-6065.2) 1.000 0.000 0.000 -0.568; 0.000 1.000 0.000 8.523; 0.000 0.000 1.000 -16.477; 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=-6034.4, old_max_log_p =-6071.3 (thresh=-6065.2) 1.016 -0.066 -0.004 5.272; 0.069 1.055 0.002 -4.692; 0.004 0.002 0.981 -16.890; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6025.5, old_max_log_p =-6034.4 (thresh=-6028.4) 1.035 -0.066 0.028 -3.022; 0.070 1.074 -0.030 -2.868; -0.026 0.038 0.962 -12.658; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6015.9, old_max_log_p =-6025.5 (thresh=-6019.5) 1.028 -0.136 0.032 6.836; 0.141 1.085 -0.061 -11.419; -0.024 0.073 0.961 -18.453; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6012.8, old_max_log_p =-6015.9 (thresh=-6009.9) 1.052 -0.103 0.001 3.945; 0.107 1.112 0.002 -16.004; 0.001 -0.002 0.945 -11.302; 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=-5989.4, old_max_log_p =-6012.8 (thresh=-6006.8) 1.053 -0.103 0.009 2.859; 0.108 1.116 0.010 -16.960; -0.009 -0.011 0.944 -9.049; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-5981.7, old_max_log_p =-5989.4 (thresh=-5983.4) 1.054 -0.103 0.009 2.714; 0.108 1.117 0.010 -17.119; -0.009 -0.011 0.943 -8.915; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-5981.3, old_max_log_p =-5981.7 (thresh=-5975.7) 1.054 -0.103 0.009 2.714; 0.108 1.116 0.010 -16.960; -0.009 -0.011 0.943 -8.915; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2185 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05404 -0.10294 0.00856 2.71407; 0.10779 1.11584 0.00979 -16.95956; -0.00883 -0.01051 0.94278 -8.91490; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.05404 -0.10294 0.00856 2.71407; 0.10779 1.11584 0.00979 -16.95956; -0.00883 -0.01051 0.94278 -8.91490; 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: 010: -log(p) = 5981.3 tol 0.000010 Resulting transform: 1.054 -0.103 0.009 2.714; 0.108 1.116 0.010 -16.960; -0.009 -0.011 0.943 -8.915; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -5981.3 (old=-6369.1) transform before final EM align: 1.054 -0.103 0.009 2.714; 0.108 1.116 0.010 -16.960; -0.009 -0.011 0.943 -8.915; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 244171 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05404 -0.10294 0.00856 2.71407; 0.10779 1.11584 0.00979 -16.95956; -0.00883 -0.01051 0.94278 -8.91490; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.05404 -0.10294 0.00856 2.71407; 0.10779 1.11584 0.00979 -16.95956; -0.00883 -0.01051 0.94278 -8.91490; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 706565.2 after pass:transform: ( 1.05, -0.10, 0.01, 2.71) ( 0.11, 1.12, 0.01, -16.96) ( -0.01, -0.01, 0.94, -8.91) dfp_em_step_func: 012: -log(p) = 706564.9 after pass:transform: ( 1.05, -0.10, 0.01, 2.71) ( 0.11, 1.12, 0.01, -16.96) ( -0.01, -0.01, 0.94, -8.91) dfp_em_step_func: 013: -log(p) = 704109.1 after pass:transform: ( 1.05, -0.11, 0.00, 2.71) ( 0.10, 1.11, 0.00, -16.96) ( -0.00, -0.00, 0.95, -8.91) dfp_em_step_func: 014: -log(p) = 703878.7 after pass:transform: ( 1.05, -0.11, 0.00, 2.71) ( 0.10, 1.11, 0.01, -16.96) ( -0.00, -0.01, 0.95, -8.91) dfp_em_step_func: 015: -log(p) = 703827.8 after pass:transform: ( 1.05, -0.11, 0.00, 2.71) ( 0.10, 1.11, 0.01, -16.96) ( -0.00, -0.01, 0.95, -8.91) 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: 017: -log(p) = 703827.8 tol 0.000000 final transform: 1.050 -0.107 0.003 2.714; 0.102 1.111 0.005 -16.960; -0.002 -0.005 0.951 -8.915; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 27 minutes and 14 seconds. #-------------------------------------- #@# CA Normalize Tue Apr 20 10:44:28 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/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/dev/average/RB_all_2008-03-26.gca'... 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=30.0 skull bounding box = (64, 51, 39) --> (194, 168, 215) using (107, 90, 127) as brain centroid... mean wm in atlas = 107, using box (91,76,105) --> (122, 104,148) to find MRI wm before smoothing, mri peak at 198 after smoothing, mri peak at 197, scaling input intensities by 0.543 scaling channel 0 by 0.543147 using 244171 sample points... INFO: compute sample coordinates transform 1.050 -0.107 0.003 2.714; 0.102 1.111 0.005 -16.960; -0.002 -0.005 0.951 -8.915; 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 (127, 49, 38) --> (192, 153, 214) Left_Cerebral_White_Matter: limiting intensities to 118.0 --> 138.0 2 of 4207 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 51, 38) --> (129, 159, 214) Right_Cerebral_White_Matter: limiting intensities to 118.0 --> 138.0 2 of 3668 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 123, 61) --> (180, 162, 118) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 138.0 0 of 656 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 124, 59) --> (132, 166, 118) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 138.0 0 of 638 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 119, 97) --> (148, 181, 130) Brain_Stem: limiting intensities to 89.0 --> 138.0 0 of 654 (0.0%) samples deleted using 9823 total control points for intensity normalization... bias field = 0.846 +- 0.024 8 of 9819 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 49, 38) --> (192, 153, 214) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 117.0 0 of 4467 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 51, 38) --> (129, 159, 214) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 117.0 2 of 3975 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 123, 61) --> (180, 162, 118) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 117.0 2 of 664 (0.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 124, 59) --> (132, 166, 118) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 117.0 0 of 650 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 119, 97) --> (148, 181, 130) Brain_Stem: limiting intensities to 72.0 --> 117.0 0 of 738 (0.0%) samples deleted using 10494 total control points for intensity normalization... bias field = 1.012 +- 0.022 31 of 10490 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 49, 38) --> (192, 153, 214) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 118.0 0 of 4449 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 51, 38) --> (129, 159, 214) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 118.0 2 of 4004 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 123, 61) --> (180, 162, 118) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 118.0 1 of 655 (0.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 124, 59) --> (132, 166, 118) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 118.0 0 of 632 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 119, 97) --> (148, 181, 130) Brain_Stem: limiting intensities to 72.0 --> 118.0 0 of 728 (0.0%) samples deleted using 10468 total control points for intensity normalization... bias field = 1.009 +- 0.020 30 of 10465 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 51 seconds. #-------------------------------------- #@# CA Reg Tue Apr 20 10:46:20 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/dev/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/dev/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.12 (predicted orig area = 7.1) 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=0.649, neg=0, invalid=766 0001: dt=129.472000, rms=0.513 (20.927%), neg=0, invalid=766 0002: dt=152.768606, rms=0.497 (3.092%), neg=0, invalid=766 0003: dt=221.952000, rms=0.491 (1.263%), neg=0, invalid=766 0004: dt=74.847458, rms=0.490 (0.252%), neg=0, invalid=766 0005: dt=517.888000, rms=0.486 (0.732%), neg=0, invalid=766 0006: dt=152.436364, rms=0.484 (0.504%), neg=0, invalid=766 0007: dt=32.368000, rms=0.484 (0.017%), neg=0, invalid=766 0008: dt=32.368000, rms=0.483 (0.019%), neg=0, invalid=766 0009: dt=32.368000, rms=0.483 (0.027%), neg=0, invalid=766 0010: dt=32.368000, rms=0.483 (0.041%), neg=0, invalid=766 0011: dt=32.368000, rms=0.483 (0.076%), neg=0, invalid=766 0012: dt=32.368000, rms=0.482 (0.112%), neg=0, invalid=766 0013: dt=32.368000, rms=0.482 (0.137%), neg=0, invalid=766 0014: dt=32.368000, rms=0.481 (0.140%), neg=0, invalid=766 0015: dt=32.368000, rms=0.480 (0.125%), neg=0, invalid=766 0016: dt=32.368000, rms=0.480 (0.105%), neg=0, invalid=766 0017: dt=32.368000, rms=0.479 (0.086%), neg=0, invalid=766 0018: dt=221.952000, rms=0.479 (0.045%), neg=0, invalid=766 0019: dt=221.952000, rms=0.478 (0.166%), neg=0, invalid=766 0020: dt=221.952000, rms=0.478 (0.023%), neg=0, invalid=766 0021: dt=221.952000, rms=0.477 (0.281%), neg=0, invalid=766 0022: dt=221.952000, rms=0.476 (0.151%), neg=0, invalid=766 0023: dt=221.952000, rms=0.475 (0.210%), neg=0, invalid=766 0024: dt=221.952000, rms=0.474 (0.232%), neg=0, invalid=766 0025: dt=221.952000, rms=0.474 (0.044%), neg=0, invalid=766 0026: dt=221.952000, rms=0.473 (0.248%), neg=0, invalid=766 0027: dt=221.952000, rms=0.472 (0.098%), neg=0, invalid=766 0028: dt=221.952000, rms=0.472 (0.061%), neg=0, invalid=766 0029: dt=443.904000, rms=0.471 (0.150%), neg=0, invalid=766 0030: dt=23.120000, rms=0.471 (0.014%), neg=0, invalid=766 0031: dt=23.120000, rms=0.471 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=766 0032: dt=32.368000, rms=0.471 (0.027%), neg=0, invalid=766 0033: dt=73.984000, rms=0.471 (0.018%), neg=0, invalid=766 0034: dt=73.984000, rms=0.471 (0.040%), neg=0, invalid=766 0035: dt=73.984000, rms=0.470 (0.056%), neg=0, invalid=766 0036: dt=73.984000, rms=0.470 (0.059%), neg=0, invalid=766 0037: dt=73.984000, rms=0.470 (0.065%), neg=0, invalid=766 0038: dt=73.984000, rms=0.470 (0.071%), neg=0, invalid=766 0039: dt=73.984000, rms=0.469 (0.063%), neg=0, invalid=766 0040: dt=73.984000, rms=0.469 (0.036%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=766 0041: dt=131.014493, rms=0.467 (0.960%), neg=0, invalid=766 0042: dt=108.269750, rms=0.461 (1.303%), neg=0, invalid=766 0043: dt=29.623762, rms=0.459 (0.281%), neg=0, invalid=766 0044: dt=99.368421, rms=0.458 (0.257%), neg=0, invalid=766 0045: dt=77.381818, rms=0.456 (0.469%), neg=0, invalid=766 0046: dt=31.104000, rms=0.455 (0.162%), neg=0, invalid=766 0047: dt=31.104000, rms=0.455 (0.068%), neg=0, invalid=766 0048: dt=31.104000, rms=0.454 (0.159%), neg=0, invalid=766 0049: dt=31.104000, rms=0.453 (0.245%), neg=0, invalid=766 0050: dt=31.104000, rms=0.452 (0.272%), neg=0, invalid=766 0051: dt=31.104000, rms=0.451 (0.270%), neg=0, invalid=766 0052: dt=31.104000, rms=0.449 (0.246%), neg=0, invalid=766 0053: dt=31.104000, rms=0.448 (0.239%), neg=0, invalid=766 0054: dt=31.104000, rms=0.447 (0.235%), neg=0, invalid=766 0055: dt=31.104000, rms=0.446 (0.207%), neg=0, invalid=766 0056: dt=31.104000, rms=0.446 (0.162%), neg=0, invalid=766 0057: dt=31.104000, rms=0.445 (0.140%), neg=0, invalid=766 0058: dt=31.104000, rms=0.444 (0.137%), neg=0, invalid=766 0059: dt=31.104000, rms=0.444 (0.130%), neg=0, invalid=766 0060: dt=31.104000, rms=0.443 (0.119%), neg=0, invalid=766 0061: dt=31.104000, rms=0.443 (0.088%), neg=0, invalid=766 0062: dt=145.152000, rms=0.443 (0.031%), neg=0, invalid=766 0063: dt=145.152000, rms=0.443 (-0.028%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=766 0064: dt=62.984127, rms=0.442 (0.119%), neg=0, invalid=766 0065: dt=22.000000, rms=0.442 (0.013%), neg=0, invalid=766 0066: dt=22.000000, rms=0.442 (0.008%), neg=0, invalid=766 0067: dt=22.000000, rms=0.442 (0.012%), neg=0, invalid=766 0068: dt=22.000000, rms=0.442 (0.013%), neg=0, invalid=766 0069: dt=22.000000, rms=0.442 (0.011%), neg=0, invalid=766 0070: dt=22.000000, rms=0.442 (0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=766 0071: dt=24.615385, rms=0.451 (0.508%), neg=0, invalid=766 0072: dt=38.400000, rms=0.449 (0.304%), neg=0, invalid=766 0073: dt=80.041775, rms=0.447 (0.610%), neg=0, invalid=766 0074: dt=15.030303, rms=0.446 (0.156%), neg=0, invalid=766 0075: dt=15.030303, rms=0.445 (0.174%), neg=0, invalid=766 0076: dt=15.030303, rms=0.445 (-0.013%), neg=0, invalid=766 0077: dt=2.800000, rms=0.445 (0.004%), neg=0, invalid=766 0078: dt=8.000000, rms=0.445 (0.011%), neg=0, invalid=766 0079: dt=153.600000, rms=0.444 (0.322%), neg=0, invalid=766 0080: dt=11.200000, rms=0.443 (0.156%), neg=0, invalid=766 0081: dt=11.200000, rms=0.443 (0.066%), neg=0, invalid=766 0082: dt=11.200000, rms=0.443 (0.043%), neg=0, invalid=766 0083: dt=11.200000, rms=0.442 (0.039%), neg=0, invalid=766 0084: dt=9.600000, rms=0.442 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=766 0085: dt=0.000000, rms=0.442 (0.003%), neg=0, invalid=766 0086: dt=0.000000, rms=0.442 (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=0.461, neg=0, invalid=766 0087: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=766 0088: dt=0.000000, rms=0.461 (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=0.500, neg=0, invalid=766 0089: dt=0.838196, rms=0.493 (1.290%), neg=0, invalid=766 0090: dt=0.485294, rms=0.493 (0.093%), neg=0, invalid=766 0091: dt=0.485294, rms=0.492 (0.039%), neg=0, invalid=766 0092: dt=0.485294, rms=0.492 (-0.088%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=766 0093: dt=0.480000, rms=0.492 (0.067%), neg=0, invalid=766 0094: dt=0.448000, rms=0.492 (0.017%), neg=0, invalid=766 0095: dt=0.448000, rms=0.492 (0.000%), neg=0, invalid=766 0096: dt=0.448000, rms=0.492 (-0.053%), 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=0.459, neg=0, invalid=766 0097: dt=0.690549, rms=0.450 (2.074%), neg=0, invalid=766 0098: dt=0.024000, rms=0.449 (0.108%), neg=0, invalid=766 0099: dt=0.024000, rms=0.449 (-0.059%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=766 0100: dt=0.005000, rms=0.449 (0.002%), neg=0, invalid=766 0101: dt=0.000000, rms=0.449 (-0.001%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.08955 (18) Left_Lateral_Ventricle (4): linear fit = 0.73 x + 0.0 (4076 voxels, overlap=0.334) Left_Lateral_Ventricle (4): linear fit = 0.73 x + 0.0 (4076 voxels, peak = 17), gca=17.4 gca peak = 0.14022 (22) mri peak = 0.13947 (17) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (3456 voxels, overlap=0.572) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (3456 voxels, peak = 16), gca=16.0 gca peak = 0.24234 (100) mri peak = 0.13311 (90) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (601 voxels, overlap=0.071) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (601 voxels, peak = 90), gca=90.0 gca peak = 0.19192 (97) mri peak = 0.10517 (90) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (560 voxels, overlap=0.175) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (560 voxels, peak = 90), gca=89.7 gca peak = 0.24007 (63) mri peak = 0.20034 (57) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (1285 voxels, overlap=0.129) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (1285 voxels, peak = 55), gca=55.1 gca peak = 0.29892 (64) mri peak = 0.16245 (59) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1297 voxels, overlap=0.708) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1297 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.07668 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (105565 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (105565 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.07493 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (110562 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (110562 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03154 (56) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (73881 voxels, overlap=0.494) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (73881 voxels, peak = 57), gca=56.7 gca peak = 0.13270 (63) mri peak = 0.03587 (56) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (73375 voxels, overlap=0.382) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (73375 voxels, peak = 55), gca=55.1 gca peak = 0.15182 (70) mri peak = 0.10608 (69) Right_Caudate (50): linear fit = 0.93 x + 0.0 (839 voxels, overlap=0.662) Right_Caudate (50): linear fit = 0.93 x + 0.0 (839 voxels, peak = 65), gca=64.8 gca peak = 0.14251 (76) mri peak = 0.10104 (70) Left_Caudate (11): linear fit = 0.90 x + 0.0 (1007 voxels, overlap=0.512) Left_Caudate (11): linear fit = 0.90 x + 0.0 (1007 voxels, peak = 68), gca=68.4 gca peak = 0.12116 (60) mri peak = 0.04848 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (43440 voxels, overlap=0.789) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (43440 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.05579 (66) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (48058 voxels, overlap=0.810) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (48058 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.15909 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12522 voxels, overlap=0.760) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12522 voxels, peak = 90), gca=90.2 gca peak = 0.21067 (87) mri peak = 0.15432 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (11038 voxels, overlap=0.867) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (11038 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.19038 (58) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (499 voxels, overlap=0.832) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (499 voxels, peak = 57), gca=57.4 gca peak = 0.39668 (62) mri peak = 0.23391 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (466 voxels, overlap=0.221) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (466 voxels, peak = 56), gca=55.8 gca peak = 0.10129 (93) mri peak = 0.05302 (86) Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (6253 voxels, overlap=0.657) Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (6253 voxels, peak = 86), gca=86.0 gca peak = 0.12071 (89) mri peak = 0.05680 (84) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (5655 voxels, overlap=0.734) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (5655 voxels, peak = 82), gca=82.3 gca peak = 0.13716 (82) mri peak = 0.06671 (79) Left_Putamen (12): linear fit = 0.95 x + 0.0 (3283 voxels, overlap=0.984) Left_Putamen (12): linear fit = 0.95 x + 0.0 (3283 voxels, peak = 78), gca=77.9 gca peak = 0.15214 (84) mri peak = 0.08203 (76) Right_Putamen (51): linear fit = 0.93 x + 0.0 (3133 voxels, overlap=0.616) Right_Putamen (51): linear fit = 0.93 x + 0.0 (3133 voxels, peak = 78), gca=77.7 gca peak = 0.08983 (85) mri peak = 0.05726 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (16904 voxels, overlap=0.872) Brain_Stem (16): linear fit = 1.00 x + 0.0 (16904 voxels, peak = 85), gca=85.0 gca peak = 0.11809 (92) mri peak = 0.07334 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1948 voxels, overlap=0.719) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1948 voxels, peak = 92), gca=92.0 gca peak = 0.12914 (94) mri peak = 0.07399 (94) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2209 voxels, overlap=0.784) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2209 voxels, peak = 92), gca=91.7 gca peak = 0.21100 (36) mri peak = 0.05089 (33) Third_Ventricle (14): linear fit = 1.05 x + 0.0 (189 voxels, overlap=0.834) Third_Ventricle (14): linear fit = 1.05 x + 0.0 (189 voxels, peak = 38), gca=37.8 gca peak = 0.13542 (27) mri peak = 0.09023 (15) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (1061 voxels, overlap=0.236) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (1061 voxels, peak = 16), gca=15.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) 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 0.90 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.83 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=0.471, neg=0, invalid=766 0102: dt=131.000000, rms=0.469 (0.432%), neg=0, invalid=766 0103: dt=129.472000, rms=0.467 (0.339%), neg=0, invalid=766 0104: dt=32.368000, rms=0.467 (0.038%), neg=0, invalid=766 0105: dt=32.368000, rms=0.467 (0.020%), neg=0, invalid=766 0106: dt=32.368000, rms=0.467 (0.026%), neg=0, invalid=766 0107: dt=32.368000, rms=0.467 (0.045%), neg=0, invalid=766 0108: dt=32.368000, rms=0.466 (0.073%), neg=0, invalid=766 0109: dt=32.368000, rms=0.466 (0.088%), neg=0, invalid=766 0110: dt=32.368000, rms=0.466 (0.077%), neg=0, invalid=766 0111: dt=32.368000, rms=0.465 (0.057%), neg=0, invalid=766 0112: dt=32.368000, rms=0.465 (0.046%), neg=0, invalid=766 0113: dt=32.368000, rms=0.465 (0.034%), neg=0, invalid=766 0114: dt=32.368000, rms=0.465 (0.031%), neg=0, invalid=766 0115: dt=32.368000, rms=0.465 (0.040%), neg=0, invalid=766 0116: dt=32.368000, rms=0.464 (0.059%), neg=0, invalid=766 0117: dt=32.368000, rms=0.464 (0.061%), neg=0, invalid=766 0118: dt=32.368000, rms=0.464 (0.052%), neg=0, invalid=766 0119: dt=32.368000, rms=0.464 (0.045%), neg=0, invalid=766 0120: dt=32.368000, rms=0.464 (0.041%), neg=0, invalid=766 0121: dt=32.368000, rms=0.463 (0.033%), neg=0, invalid=766 0122: dt=32.368000, rms=0.463 (0.025%), neg=0, invalid=766 0123: dt=32.368000, rms=0.463 (0.026%), neg=0, invalid=766 0124: dt=32.368000, rms=0.463 (0.030%), neg=0, invalid=766 0125: dt=32.368000, rms=0.463 (0.030%), neg=0, invalid=766 0126: dt=32.368000, rms=0.463 (0.025%), neg=0, invalid=766 0127: dt=32.368000, rms=0.463 (0.023%), neg=0, invalid=766 0128: dt=110.976000, rms=0.463 (0.008%), neg=0, invalid=766 0129: dt=110.976000, rms=0.462 (0.032%), neg=0, invalid=766 0130: dt=110.976000, rms=0.462 (0.024%), neg=0, invalid=766 0131: dt=110.976000, rms=0.462 (0.019%), neg=0, invalid=766 0132: dt=129.472000, rms=0.462 (0.030%), neg=0, invalid=766 0133: dt=8.092000, rms=0.462 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=766 0134: dt=129.472000, rms=0.462 (0.106%), neg=0, invalid=766 0135: dt=129.472000, rms=0.461 (0.039%), neg=0, invalid=766 0136: dt=129.472000, rms=0.461 (0.011%), neg=0, invalid=766 0137: dt=129.472000, rms=0.461 (0.049%), neg=0, invalid=766 0138: dt=129.472000, rms=0.461 (0.041%), neg=0, invalid=766 0139: dt=129.472000, rms=0.461 (0.027%), neg=0, invalid=766 0140: dt=129.472000, rms=0.461 (0.031%), neg=0, invalid=766 0141: dt=129.472000, rms=0.460 (0.055%), neg=0, invalid=766 0142: dt=129.472000, rms=0.460 (0.036%), neg=0, invalid=766 0143: dt=129.472000, rms=0.460 (0.028%), neg=0, invalid=766 0144: dt=129.472000, rms=0.460 (0.052%), neg=0, invalid=766 0145: dt=129.472000, rms=0.460 (0.050%), neg=0, invalid=766 0146: dt=129.472000, rms=0.460 (0.034%), neg=0, invalid=766 0147: dt=129.472000, rms=0.459 (0.039%), neg=0, invalid=766 0148: dt=129.472000, rms=0.459 (0.037%), neg=0, invalid=766 0149: dt=129.472000, rms=0.459 (0.028%), neg=0, invalid=766 0150: dt=129.472000, rms=0.459 (0.028%), neg=0, invalid=766 0151: dt=129.472000, rms=0.459 (0.040%), neg=0, invalid=766 0152: dt=129.472000, rms=0.459 (0.029%), neg=0, invalid=766 0153: dt=129.472000, rms=0.459 (0.020%), neg=0, invalid=766 0154: dt=129.472000, rms=0.458 (0.031%), neg=0, invalid=766 0155: dt=129.472000, rms=0.458 (0.030%), neg=0, invalid=766 0156: dt=129.472000, rms=0.458 (0.022%), neg=0, invalid=766 0157: dt=129.472000, rms=0.458 (0.020%), neg=0, invalid=766 0158: dt=129.472000, rms=0.458 (0.003%), neg=0, invalid=766 0159: dt=129.472000, rms=0.458 (0.004%), neg=0, invalid=766 0160: dt=129.472000, rms=0.458 (0.002%), neg=0, invalid=766 0161: dt=129.472000, rms=0.458 (0.009%), neg=0, invalid=766 0162: dt=129.472000, rms=0.458 (0.011%), neg=0, invalid=766 0163: dt=129.472000, rms=0.458 (0.008%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=766 0164: dt=100.790419, rms=0.456 (0.354%), neg=0, invalid=766 0165: dt=90.689362, rms=0.454 (0.435%), neg=0, invalid=766 0166: dt=25.920000, rms=0.454 (0.148%), neg=0, invalid=766 0167: dt=124.416000, rms=0.453 (0.263%), neg=0, invalid=766 0168: dt=23.789474, rms=0.452 (0.136%), neg=0, invalid=766 0169: dt=103.680000, rms=0.451 (0.154%), neg=0, invalid=766 0170: dt=31.104000, rms=0.451 (0.128%), neg=0, invalid=766 0171: dt=31.104000, rms=0.450 (0.051%), neg=0, invalid=766 0172: dt=43.200000, rms=0.450 (0.073%), neg=0, invalid=766 0173: dt=38.400000, rms=0.450 (0.047%), neg=0, invalid=766 0174: dt=38.400000, rms=0.450 (0.077%), neg=0, invalid=766 0175: dt=38.400000, rms=0.449 (0.093%), neg=0, invalid=766 0176: dt=38.400000, rms=0.449 (0.089%), neg=0, invalid=766 0177: dt=38.400000, rms=0.448 (0.157%), neg=0, invalid=766 0178: dt=38.400000, rms=0.447 (0.155%), neg=0, invalid=766 0179: dt=38.400000, rms=0.447 (0.158%), neg=0, invalid=766 0180: dt=38.400000, rms=0.446 (0.085%), neg=0, invalid=766 0181: dt=38.400000, rms=0.446 (0.121%), neg=0, invalid=766 0182: dt=38.400000, rms=0.445 (0.133%), neg=0, invalid=766 0183: dt=38.400000, rms=0.445 (0.104%), neg=0, invalid=766 0184: dt=38.400000, rms=0.444 (0.049%), neg=0, invalid=766 0185: dt=38.400000, rms=0.444 (0.100%), neg=0, invalid=766 0186: dt=38.400000, rms=0.443 (0.119%), neg=0, invalid=766 0187: dt=38.400000, rms=0.443 (0.091%), neg=0, invalid=766 0188: dt=38.400000, rms=0.443 (0.057%), neg=0, invalid=766 0189: dt=38.400000, rms=0.442 (0.104%), neg=0, invalid=766 0190: dt=38.400000, rms=0.442 (0.106%), neg=0, invalid=766 0191: dt=38.400000, rms=0.442 (0.081%), neg=0, invalid=766 0192: dt=38.400000, rms=0.441 (0.064%), neg=0, invalid=766 0193: dt=38.400000, rms=0.441 (0.095%), neg=0, invalid=766 0194: dt=38.400000, rms=0.440 (0.085%), neg=0, invalid=766 0195: dt=38.400000, rms=0.440 (0.065%), neg=0, invalid=766 0196: dt=38.400000, rms=0.440 (0.057%), neg=0, invalid=766 0197: dt=38.400000, rms=0.440 (0.078%), neg=0, invalid=766 0198: dt=38.400000, rms=0.439 (0.074%), neg=0, invalid=766 0199: dt=38.400000, rms=0.439 (0.062%), neg=0, invalid=766 0200: dt=38.400000, rms=0.439 (0.048%), neg=0, invalid=766 0201: dt=38.400000, rms=0.439 (0.057%), neg=0, invalid=766 0202: dt=38.400000, rms=0.438 (0.050%), neg=0, invalid=766 0203: dt=38.400000, rms=0.438 (0.046%), neg=0, invalid=766 0204: dt=38.400000, rms=0.438 (0.047%), neg=0, invalid=766 0205: dt=38.400000, rms=0.438 (0.046%), neg=0, invalid=766 0206: dt=38.400000, rms=0.437 (0.041%), neg=0, invalid=766 0207: dt=38.400000, rms=0.437 (0.043%), neg=0, invalid=766 0208: dt=38.400000, rms=0.437 (0.027%), neg=0, invalid=766 0209: dt=38.400000, rms=0.437 (0.037%), neg=0, invalid=766 0210: dt=38.400000, rms=0.437 (0.047%), neg=0, invalid=766 0211: dt=38.400000, rms=0.437 (0.034%), neg=0, invalid=766 0212: dt=38.400000, rms=0.437 (0.027%), neg=0, invalid=766 0213: dt=38.400000, rms=0.436 (0.034%), neg=0, invalid=766 0214: dt=38.400000, rms=0.436 (0.030%), neg=0, invalid=766 0215: dt=38.400000, rms=0.436 (0.019%), neg=0, invalid=766 0216: dt=38.400000, rms=0.436 (0.020%), neg=0, invalid=766 0217: dt=38.400000, rms=0.436 (0.034%), neg=0, invalid=766 0218: dt=38.400000, rms=0.436 (0.019%), neg=0, invalid=766 0219: dt=38.400000, rms=0.436 (0.017%), neg=0, invalid=766 0220: dt=145.152000, rms=0.436 (0.031%), neg=0, invalid=766 0221: dt=0.000000, rms=0.436 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=766 0222: dt=36.288000, rms=0.436 (0.038%), neg=0, invalid=766 0223: dt=145.152000, rms=0.435 (0.124%), neg=0, invalid=766 0224: dt=9.072000, rms=0.435 (0.013%), neg=0, invalid=766 0225: dt=9.072000, rms=0.435 (-0.004%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=766 0226: dt=53.021898, rms=0.435 (0.666%), neg=0, invalid=766 0227: dt=15.775701, rms=0.432 (0.752%), neg=0, invalid=766 0228: dt=9.600000, rms=0.431 (0.134%), neg=0, invalid=766 0229: dt=63.123288, rms=0.429 (0.563%), neg=0, invalid=766 0230: dt=14.760563, rms=0.427 (0.374%), neg=0, invalid=766 0231: dt=14.564103, rms=0.426 (0.262%), neg=0, invalid=766 0232: dt=11.200000, rms=0.425 (0.113%), neg=0, invalid=766 0233: dt=13.454545, rms=0.425 (0.132%), neg=0, invalid=766 0234: dt=11.200000, rms=0.425 (0.096%), neg=0, invalid=766 0235: dt=14.666667, rms=0.424 (0.111%), neg=0, invalid=766 0236: dt=11.200000, rms=0.424 (0.095%), neg=0, invalid=766 0237: dt=12.363636, rms=0.423 (0.092%), neg=0, invalid=766 0238: dt=11.636364, rms=0.423 (0.090%), neg=0, invalid=766 0239: dt=11.636364, rms=0.423 (0.079%), neg=0, invalid=766 0240: dt=11.428571, rms=0.422 (0.075%), neg=0, invalid=766 0241: dt=11.555556, rms=0.422 (0.082%), neg=0, invalid=766 0242: dt=13.333333, rms=0.422 (0.069%), neg=0, invalid=766 0243: dt=11.200000, rms=0.421 (0.077%), neg=0, invalid=766 0244: dt=11.272727, rms=0.421 (0.063%), neg=0, invalid=766 0245: dt=11.200000, rms=0.421 (0.071%), neg=0, invalid=766 0246: dt=11.500000, rms=0.420 (0.055%), neg=0, invalid=766 0247: dt=11.200000, rms=0.420 (0.066%), neg=0, invalid=766 0248: dt=12.923077, rms=0.420 (0.057%), neg=0, invalid=766 0249: dt=11.368421, rms=0.420 (0.062%), neg=0, invalid=766 0250: dt=11.200000, rms=0.419 (0.051%), neg=0, invalid=766 0251: dt=11.200000, rms=0.419 (0.056%), neg=0, invalid=766 0252: dt=11.500000, rms=0.419 (0.049%), neg=0, invalid=766 0253: dt=11.500000, rms=0.419 (0.051%), neg=0, invalid=766 0254: dt=11.500000, rms=0.418 (0.092%), neg=0, invalid=766 0255: dt=11.500000, rms=0.418 (0.127%), neg=0, invalid=766 0256: dt=11.500000, rms=0.417 (0.168%), neg=0, invalid=766 0257: dt=11.500000, rms=0.417 (0.161%), neg=0, invalid=766 0258: dt=11.500000, rms=0.416 (0.185%), neg=0, invalid=766 0259: dt=11.500000, rms=0.415 (0.193%), neg=0, invalid=766 0260: dt=11.500000, rms=0.414 (0.201%), neg=0, invalid=766 0261: dt=11.500000, rms=0.413 (0.176%), neg=0, invalid=766 0262: dt=11.500000, rms=0.413 (0.194%), neg=0, invalid=766 0263: dt=11.500000, rms=0.412 (0.155%), neg=0, invalid=766 0264: dt=11.500000, rms=0.411 (0.157%), neg=0, invalid=766 0265: dt=11.500000, rms=0.411 (0.134%), neg=0, invalid=766 0266: dt=11.500000, rms=0.410 (0.134%), neg=0, invalid=766 0267: dt=11.500000, rms=0.410 (0.112%), neg=0, invalid=766 0268: dt=11.500000, rms=0.409 (0.121%), neg=0, invalid=766 0269: dt=11.500000, rms=0.409 (0.093%), neg=0, invalid=766 0270: dt=11.500000, rms=0.408 (0.095%), neg=0, invalid=766 0271: dt=11.500000, rms=0.408 (0.082%), neg=0, invalid=766 0272: dt=11.500000, rms=0.408 (0.080%), neg=0, invalid=766 0273: dt=11.500000, rms=0.408 (0.069%), neg=0, invalid=766 0274: dt=11.500000, rms=0.407 (0.069%), neg=0, invalid=766 0275: dt=11.500000, rms=0.407 (0.046%), neg=0, invalid=766 0276: dt=11.500000, rms=0.407 (0.058%), neg=0, invalid=766 0277: dt=11.500000, rms=0.407 (0.043%), neg=0, invalid=766 0278: dt=11.500000, rms=0.406 (0.047%), neg=0, invalid=766 0279: dt=11.500000, rms=0.406 (0.042%), neg=0, invalid=766 0280: dt=11.500000, rms=0.406 (0.040%), neg=0, invalid=766 0281: dt=11.500000, rms=0.406 (0.031%), neg=0, invalid=766 0282: dt=11.500000, rms=0.406 (0.031%), neg=0, invalid=766 0283: dt=11.500000, rms=0.406 (0.039%), neg=0, invalid=766 0284: dt=11.500000, rms=0.406 (0.024%), neg=0, invalid=766 0285: dt=11.500000, rms=0.406 (0.025%), neg=0, invalid=766 0286: dt=11.500000, rms=0.405 (0.021%), neg=0, invalid=766 0287: dt=11.200000, rms=0.405 (0.014%), neg=0, invalid=766 0288: dt=11.200000, rms=0.405 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=766 0289: dt=32.000000, rms=0.405 (0.114%), neg=0, invalid=766 0290: dt=6.857143, rms=0.405 (0.044%), neg=0, invalid=766 0291: dt=6.857143, rms=0.405 (0.021%), neg=0, invalid=766 0292: dt=6.857143, rms=0.405 (0.027%), neg=0, invalid=766 0293: dt=6.857143, rms=0.404 (0.027%), neg=0, invalid=766 0294: dt=6.857143, rms=0.404 (0.025%), neg=0, invalid=766 0295: dt=6.857143, rms=0.404 (0.022%), neg=0, invalid=766 0296: dt=19.200000, rms=0.404 (0.003%), neg=0, invalid=766 0297: dt=19.200000, rms=0.404 (-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=0.414, neg=0, invalid=766 0298: dt=1.008000, rms=0.414 (0.012%), neg=0, invalid=766 0299: dt=0.720000, rms=0.414 (0.002%), neg=0, invalid=766 0300: dt=0.720000, rms=0.414 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=766 0301: dt=1.008000, rms=0.414 (0.010%), neg=0, invalid=766 0302: dt=0.720000, rms=0.414 (0.004%), neg=0, invalid=766 0303: dt=0.720000, rms=0.414 (-0.004%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.432, neg=0, invalid=766 0304: dt=1.792000, rms=0.429 (0.699%), neg=0, invalid=766 0305: dt=0.448000, rms=0.429 (0.042%), neg=0, invalid=766 0306: dt=0.448000, rms=0.429 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=766 0307: dt=1.093023, rms=0.429 (0.093%), neg=0, invalid=766 0308: dt=0.448000, rms=0.429 (0.006%), neg=0, invalid=766 0309: dt=0.448000, rms=0.429 (-0.002%), 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=0.414, neg=0, invalid=766 0310: dt=0.448000, rms=0.405 (2.239%), neg=0, invalid=766 0311: dt=1.280000, rms=0.401 (0.966%), neg=0, invalid=766 0312: dt=0.112000, rms=0.401 (0.002%), neg=0, invalid=766 0313: dt=0.112000, rms=0.401 (0.012%), neg=0, invalid=766 0314: dt=0.112000, rms=0.401 (0.011%), neg=0, invalid=766 0315: dt=0.112000, rms=0.401 (0.006%), neg=0, invalid=766 0316: dt=0.006000, rms=0.401 (0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=766 0317: dt=0.448000, rms=0.399 (0.320%), neg=0, invalid=766 0318: dt=0.611111, rms=0.399 (0.050%), neg=0, invalid=766 0319: dt=1.536000, rms=0.399 (0.055%), neg=0, invalid=766 0320: dt=0.112000, rms=0.399 (0.008%), neg=0, invalid=766 0321: dt=0.112000, rms=0.399 (0.009%), neg=0, invalid=766 0322: dt=0.112000, rms=0.399 (0.015%), neg=0, invalid=766 0323: dt=0.112000, rms=0.399 (0.003%), neg=0, invalid=766 0324: dt=0.112000, rms=0.399 (0.010%), neg=0, invalid=766 0325: dt=0.112000, rms=0.399 (0.001%), neg=0, invalid=766 0326: dt=0.448000, rms=0.399 (0.010%), neg=0, invalid=766 0327: dt=1.792000, rms=0.399 (0.016%), neg=0, invalid=766 0328: dt=0.384000, rms=0.399 (0.009%), 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 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.397, neg=0, invalid=766 0329: dt=32.368000, rms=0.398 (-0.277%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=766 0330: dt=110.976000, rms=0.398 (0.035%), neg=0, invalid=766 0331: dt=129.472000, rms=0.398 (0.029%), neg=0, invalid=766 0332: dt=129.472000, rms=0.398 (-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=0.398, neg=0, invalid=766 0333: dt=36.288000, rms=0.398 (0.027%), neg=0, invalid=766 0334: dt=36.288000, rms=0.398 (0.014%), neg=0, invalid=766 0335: dt=36.288000, rms=0.398 (0.014%), neg=0, invalid=766 0336: dt=36.288000, rms=0.398 (0.013%), neg=0, invalid=766 0337: dt=36.288000, rms=0.398 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=766 0338: dt=103.680000, rms=0.397 (0.128%), neg=0, invalid=766 0339: dt=82.944000, rms=0.397 (0.080%), neg=0, invalid=766 0340: dt=31.104000, rms=0.397 (0.011%), neg=0, invalid=766 0341: dt=31.104000, rms=0.397 (0.011%), neg=0, invalid=766 0342: dt=31.104000, rms=0.397 (0.019%), neg=0, invalid=766 0343: dt=31.104000, rms=0.397 (0.026%), neg=0, invalid=766 0344: dt=31.104000, rms=0.397 (0.031%), neg=0, invalid=766 0345: dt=31.104000, rms=0.397 (0.031%), neg=0, invalid=766 0346: dt=31.104000, rms=0.397 (0.027%), neg=0, invalid=766 0347: dt=31.104000, rms=0.396 (0.022%), neg=0, invalid=766 0348: dt=31.104000, rms=0.396 (0.021%), neg=0, invalid=766 0349: dt=580.608000, rms=0.396 (0.100%), neg=0, invalid=766 0350: dt=36.288000, rms=0.396 (0.019%), neg=0, invalid=766 0351: dt=36.288000, rms=0.396 (0.005%), neg=0, invalid=766 0352: dt=36.288000, rms=0.396 (0.005%), neg=0, invalid=766 0353: dt=36.288000, rms=0.396 (0.008%), neg=0, invalid=766 0354: dt=36.288000, rms=0.396 (0.014%), neg=0, invalid=766 0355: dt=36.288000, rms=0.396 (0.017%), neg=0, invalid=766 0356: dt=36.288000, rms=0.396 (0.017%), neg=0, invalid=766 0357: dt=36.288000, rms=0.396 (0.019%), neg=0, invalid=766 0358: dt=36.288000, rms=0.395 (0.021%), neg=0, invalid=766 0359: dt=36.288000, rms=0.395 (0.021%), neg=0, invalid=766 0360: dt=331.776000, rms=0.395 (0.017%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.396, neg=0, invalid=766 0361: dt=62.545455, rms=0.394 (0.473%), neg=0, invalid=766 0362: dt=44.800000, rms=0.392 (0.386%), neg=0, invalid=766 0363: dt=36.363636, rms=0.391 (0.230%), neg=0, invalid=766 0364: dt=38.037736, rms=0.391 (0.146%), neg=0, invalid=766 0365: dt=44.800000, rms=0.390 (0.185%), neg=0, invalid=766 0366: dt=23.600000, rms=0.390 (0.101%), neg=0, invalid=766 0367: dt=153.600000, rms=0.388 (0.300%), neg=0, invalid=766 0368: dt=14.080000, rms=0.388 (0.163%), neg=0, invalid=766 0369: dt=32.000000, rms=0.388 (0.038%), neg=0, invalid=766 0370: dt=32.000000, rms=0.387 (0.076%), neg=0, invalid=766 0371: dt=32.000000, rms=0.387 (0.099%), neg=0, invalid=766 0372: dt=32.000000, rms=0.387 (0.118%), neg=0, invalid=766 0373: dt=32.000000, rms=0.386 (0.134%), neg=0, invalid=766 0374: dt=32.000000, rms=0.385 (0.171%), neg=0, invalid=766 0375: dt=32.000000, rms=0.385 (0.154%), neg=0, invalid=766 0376: dt=32.000000, rms=0.384 (0.138%), neg=0, invalid=766 0377: dt=32.000000, rms=0.384 (0.118%), neg=0, invalid=766 0378: dt=32.000000, rms=0.383 (0.132%), neg=0, invalid=766 0379: dt=32.000000, rms=0.383 (0.118%), neg=0, invalid=766 0380: dt=32.000000, rms=0.382 (0.096%), neg=0, invalid=766 0381: dt=32.000000, rms=0.382 (0.076%), neg=0, invalid=766 0382: dt=32.000000, rms=0.382 (0.078%), neg=0, invalid=766 0383: dt=32.000000, rms=0.382 (0.078%), neg=0, invalid=766 0384: dt=32.000000, rms=0.381 (0.059%), neg=0, invalid=766 0385: dt=32.000000, rms=0.381 (0.044%), neg=0, invalid=766 0386: dt=32.000000, rms=0.381 (0.042%), neg=0, invalid=766 0387: dt=32.000000, rms=0.381 (0.049%), neg=0, invalid=766 0388: dt=32.000000, rms=0.381 (0.041%), neg=0, invalid=766 0389: dt=32.000000, rms=0.381 (0.031%), neg=0, invalid=766 0390: dt=32.000000, rms=0.380 (0.026%), neg=0, invalid=766 0391: dt=32.000000, rms=0.380 (0.034%), neg=0, invalid=766 0392: dt=32.000000, rms=0.380 (0.034%), neg=0, invalid=766 0393: dt=32.000000, rms=0.380 (0.027%), neg=0, invalid=766 0394: dt=32.000000, rms=0.380 (0.021%), neg=0, invalid=766 0395: dt=32.000000, rms=0.380 (0.025%), neg=0, invalid=766 0396: dt=32.000000, rms=0.380 (0.029%), neg=0, invalid=766 0397: dt=32.000000, rms=0.380 (0.024%), neg=0, invalid=766 0398: dt=32.000000, rms=0.380 (0.018%), neg=0, invalid=766 0399: dt=409.600000, rms=0.380 (0.022%), neg=0, invalid=766 0400: dt=9.600000, rms=0.380 (0.004%), neg=0, invalid=766 0401: dt=9.600000, rms=0.380 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=766 0402: dt=38.400000, rms=0.379 (0.140%), neg=0, invalid=766 0403: dt=44.800000, rms=0.379 (0.119%), neg=0, invalid=766 0404: dt=11.200000, rms=0.379 (0.010%), neg=0, invalid=766 0405: dt=11.200000, rms=0.378 (0.007%), neg=0, invalid=766 0406: dt=11.200000, rms=0.378 (0.011%), neg=0, invalid=766 0407: dt=11.200000, rms=0.378 (0.016%), neg=0, invalid=766 0408: dt=11.200000, rms=0.378 (0.025%), neg=0, invalid=766 0409: dt=11.200000, rms=0.378 (0.030%), neg=0, invalid=766 0410: dt=11.200000, rms=0.378 (0.028%), neg=0, invalid=766 0411: dt=11.200000, rms=0.378 (0.021%), neg=0, invalid=766 0412: dt=11.200000, rms=0.378 (0.015%), neg=0, invalid=766 0413: dt=8.000000, rms=0.378 (0.000%), neg=0, invalid=766 0414: dt=8.000000, rms=0.378 (0.001%), neg=0, invalid=766 0415: dt=8.000000, rms=0.378 (0.002%), neg=0, invalid=766 0416: dt=8.000000, rms=0.378 (0.003%), neg=0, invalid=766 0417: dt=8.000000, rms=0.378 (0.005%), neg=0, invalid=766 0418: dt=8.000000, rms=0.378 (0.007%), neg=0, invalid=766 0419: dt=8.000000, rms=0.378 (0.008%), neg=0, invalid=766 0420: dt=8.000000, rms=0.378 (0.008%), neg=0, invalid=766 0421: dt=8.000000, rms=0.378 (0.008%), neg=0, invalid=766 0422: dt=8.000000, rms=0.378 (0.007%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 0423: dt=1.008000, rms=0.383 (0.008%), neg=0, invalid=766 0424: dt=1.008000, rms=0.382 (0.003%), neg=0, invalid=766 0425: dt=1.008000, rms=0.382 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.382, neg=0, invalid=766 0426: dt=2.304000, rms=0.382 (0.014%), neg=0, invalid=766 0427: dt=1.008000, rms=0.382 (0.002%), neg=0, invalid=766 0428: dt=1.008000, rms=0.382 (-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=0.390, neg=0, invalid=766 0429: dt=1.536000, rms=0.389 (0.341%), neg=0, invalid=766 0430: dt=0.448000, rms=0.389 (0.014%), neg=0, invalid=766 0431: dt=0.448000, rms=0.389 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 0432: dt=1.280000, rms=0.389 (0.073%), neg=0, invalid=766 0433: dt=0.448000, rms=0.389 (0.006%), neg=0, invalid=766 0434: dt=0.448000, rms=0.389 (0.001%), neg=0, invalid=766 0435: dt=0.448000, rms=0.389 (-0.016%), 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=0.384, neg=0, invalid=766 0436: dt=1.792000, rms=0.364 (5.138%), neg=0, invalid=766 0437: dt=0.000000, rms=0.364 (0.000%), neg=0, invalid=766 0438: dt=0.050000, rms=0.364 (-0.131%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.364, neg=0, invalid=766 0439: dt=0.000000, rms=0.364 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 3 hours, 29 minutes and 34 seconds. #-------------------------------------- #@# CA Reg Inv Tue Apr 20 14:15:54 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 Apr 20 14:16:55 EDT 2010 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11089307 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 7 seconds. #-------------------------------------- #@# SkullLTA Tue Apr 20 14:18:03 EDT 2010 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/dev/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/dev/average/RB_all_withskull_2008-03-26.gca'... 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=12.0 skull bounding box = (62, 49, 37) --> (195, 170, 217) using (106, 89, 127) as brain centroid... mean wm in atlas = 126, using box (90,74,105) --> (122, 103,149) to find MRI wm before smoothing, mri peak at 198 after smoothing, mri peak at 196, scaling input intensities by 0.643 scaling channel 0 by 0.642857 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10376.2, old_max_log_p =-10437.3 (thresh=-10426.8) 1.207 -0.123 0.004 -8.243; 0.102 1.106 -0.386 23.772; 0.040 0.452 0.947 -72.430; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10374.3, old_max_log_p =-10376.2 (thresh=-10365.8) 1.283 -0.174 -0.135 5.984; 0.114 1.242 -0.279 -7.674; 0.183 0.285 0.981 -74.284; 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=-10369.8, old_max_log_p =-10374.3 (thresh=-10363.9) 1.289 -0.156 -0.104 -6.570; 0.098 1.243 -0.351 1.537; 0.144 0.354 0.929 -65.575; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10364.1, old_max_log_p =-10369.8 (thresh=-10359.4) 1.282 -0.193 -0.110 -0.672; 0.126 1.227 -0.375 3.417; 0.168 0.382 0.920 -71.760; 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 1.28225 -0.19257 -0.10964 -0.67219; 0.12577 1.22692 -0.37539 3.41736; 0.16817 0.38219 0.91971 -71.76016; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.28225 -0.19257 -0.10964 -0.67219; 0.12577 1.22692 -0.37539 3.41736; 0.16817 0.38219 0.91971 -71.76016; 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: 005: -log(p) = 10364.1 tol 0.000010 Resulting transform: 1.282 -0.193 -0.110 -0.672; 0.126 1.227 -0.375 3.417; 0.168 0.382 0.920 -71.760; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10364.1 (old=-10437.3) transform before final EM align: 1.282 -0.193 -0.110 -0.672; 0.126 1.227 -0.375 3.417; 0.168 0.382 0.920 -71.760; 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 1.28225 -0.19257 -0.10964 -0.67219; 0.12577 1.22692 -0.37539 3.41736; 0.16817 0.38219 0.91971 -71.76016; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.28225 -0.19257 -0.10964 -0.67219; 0.12577 1.22692 -0.37539 3.41736; 0.16817 0.38219 0.91971 -71.76016; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 006: -log(p) = 1146754.9 after pass:transform: ( 1.28, -0.19, -0.11, -0.67) ( 0.13, 1.23, -0.38, 3.42) ( 0.17, 0.38, 0.92, -71.76) dfp_em_step_func: 007: -log(p) = 1146753.1 after pass:transform: ( 1.28, -0.19, -0.11, -0.67) ( 0.13, 1.23, -0.38, 3.42) ( 0.17, 0.38, 0.92, -71.76) 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: 008: -log(p) = 1146752.9 after pass:transform: ( 1.28, -0.19, -0.11, -0.67) ( 0.13, 1.23, -0.38, 3.42) ( 0.17, 0.38, 0.92, -71.76) 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: 010: -log(p) = 1146752.9 tol 0.000000 final transform: 1.282 -0.193 -0.110 -0.672; 0.126 1.227 -0.375 3.417; 0.168 0.382 0.920 -71.760; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 24 minutes and 4 seconds. #-------------------------------------- #@# SubCort Seg Tue Apr 20 14:42:07 EDT 2010 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/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/dev/average/RB_all_2008-03-26.gca... 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/dev/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 = 0.16984 (18) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (2188 voxels, overlap=0.289) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (2188 voxels, peak = 17), gca=16.9 gca peak = 0.14982 (20) mri peak = 0.20941 (17) Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (2119 voxels, overlap=0.540) Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (2119 voxels, peak = 16), gca=15.5 gca peak = 0.28003 (97) mri peak = 0.18527 (95) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (421 voxels, overlap=0.482) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (421 voxels, peak = 92), gca=92.2 gca peak = 0.18160 (96) mri peak = 0.20925 (94) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (454 voxels, overlap=0.688) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (454 voxels, peak = 91), gca=91.2 gca peak = 0.27536 (62) mri peak = 0.20269 (57) Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (1329 voxels, overlap=0.457) Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (1329 voxels, peak = 56), gca=55.8 gca peak = 0.32745 (63) mri peak = 0.18176 (59) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1217 voxels, overlap=0.587) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (1217 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.11941 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (49854 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (49854 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.10967 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (53142 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (53142 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04753 (60) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (74307 voxels, overlap=0.857) Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (74307 voxels, peak = 60), gca=59.8 gca peak = 0.08598 (64) mri peak = 0.04506 (60) Right_Cerebral_Cortex (42): linear fit = 0.93 x + 0.0 (74558 voxels, overlap=0.788) Right_Cerebral_Cortex (42): linear fit = 0.93 x + 0.0 (74558 voxels, peak = 59), gca=59.2 gca peak = 0.24164 (71) mri peak = 0.10441 (69) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1177 voxels, overlap=0.999) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1177 voxels, peak = 69), gca=69.2 gca peak = 0.18227 (75) mri peak = 0.11301 (70) Left_Caudate (11): linear fit = 0.88 x + 0.0 (1303 voxels, overlap=0.312) Left_Caudate (11): linear fit = 0.88 x + 0.0 (1303 voxels, peak = 66), gca=65.6 gca peak = 0.10629 (62) mri peak = 0.08383 (67) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (32589 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (32589 voxels, peak = 67), gca=66.7 gca peak = 0.11668 (59) mri peak = 0.08660 (66) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (37168 voxels, overlap=0.739) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (37168 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.18200 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12782 voxels, overlap=0.814) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12782 voxels, peak = 90), gca=90.2 gca peak = 0.16819 (86) mri peak = 0.17546 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (10952 voxels, overlap=0.895) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (10952 voxels, peak = 88), gca=88.2 gca peak = 0.41688 (64) mri peak = 0.17326 (58) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (531 voxels, overlap=0.583) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (531 voxels, peak = 59), gca=59.2 gca peak = 0.42394 (62) mri peak = 0.15599 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (609 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (609 voxels, peak = 56), gca=55.8 gca peak = 0.10041 (96) mri peak = 0.06726 (86) Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (4728 voxels, overlap=0.497) Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (4728 voxels, peak = 89), gca=88.8 gca peak = 0.13978 (88) mri peak = 0.06932 (84) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4498 voxels, overlap=0.743) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4498 voxels, peak = 84), gca=83.6 gca peak = 0.08514 (81) mri peak = 0.07204 (72) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2693 voxels, overlap=0.674) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2693 voxels, peak = 77), gca=76.9 gca peak = 0.09624 (82) mri peak = 0.09590 (73) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2440 voxels, overlap=0.650) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2440 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.07121 (89) Brain_Stem (16): linear fit = 0.98 x + 0.0 (13845 voxels, overlap=0.783) Brain_Stem (16): linear fit = 0.98 x + 0.0 (13845 voxels, peak = 86), gca=85.8 gca peak = 0.12757 (95) mri peak = 0.10086 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1735 voxels, overlap=0.802) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1735 voxels, peak = 95), gca=95.0 gca peak = 0.17004 (92) mri peak = 0.08358 (94) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1998 voxels, overlap=0.871) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1998 voxels, peak = 90), gca=89.7 gca peak = 0.21361 (36) mri peak = 0.07330 (33) Third_Ventricle (14): linear fit = 0.93 x + 0.0 (181 voxels, overlap=0.717) Third_Ventricle (14): linear fit = 0.93 x + 0.0 (181 voxels, peak = 33), gca=33.3 gca peak = 0.26069 (23) mri peak = 0.21952 (15) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (931 voxels, overlap=0.590) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (931 voxels, peak = 14), gca=13.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) 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 1.02 x + 0.0 estimating mean csf scale to be 0.78 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.22507 (17) mri peak = 0.16984 (18) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2188 voxels, overlap=0.961) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2188 voxels, peak = 17), gca=17.0 gca peak = 0.21526 (16) mri peak = 0.20941 (17) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (2119 voxels, overlap=0.886) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (2119 voxels, peak = 16), gca=16.0 gca peak = 0.25848 (93) mri peak = 0.18527 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (421 voxels, overlap=0.998) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (421 voxels, peak = 93), gca=93.0 gca peak = 0.17548 (91) mri peak = 0.20925 (94) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (454 voxels, overlap=0.993) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (454 voxels, peak = 93), gca=93.3 gca peak = 0.34454 (56) mri peak = 0.20269 (57) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1329 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1329 voxels, peak = 56), gca=56.0 gca peak = 0.30366 (58) mri peak = 0.18176 (59) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1217 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1217 voxels, peak = 58), gca=58.0 gca peak = 0.08345 (108) mri peak = 0.11941 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (49854 voxels, overlap=0.652) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (49854 voxels, peak = 108), gca=108.0 gca peak = 0.08551 (108) mri peak = 0.10967 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (53142 voxels, overlap=0.668) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (53142 voxels, peak = 108), gca=108.0 gca peak = 0.08243 (60) mri peak = 0.04753 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (74307 voxels, overlap=0.967) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (74307 voxels, peak = 62), gca=61.5 gca peak = 0.09125 (59) mri peak = 0.04506 (60) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (74558 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (74558 voxels, peak = 60), gca=60.5 gca peak = 0.27446 (72) mri peak = 0.10441 (69) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1177 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1177 voxels, peak = 70), gca=70.2 gca peak = 0.17569 (65) mri peak = 0.11301 (70) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1303 voxels, overlap=0.993) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1303 voxels, peak = 65), gca=65.0 gca peak = 0.09762 (66) mri peak = 0.08383 (67) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (32589 voxels, overlap=0.909) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (32589 voxels, peak = 66), gca=66.0 gca peak = 0.12122 (64) mri peak = 0.08660 (66) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (37168 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (37168 voxels, peak = 64), gca=64.0 gca peak = 0.16635 (89) mri peak = 0.18200 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (12782 voxels, overlap=0.893) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (12782 voxels, peak = 89), gca=89.0 gca peak = 0.14599 (89) mri peak = 0.17546 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (10952 voxels, overlap=0.895) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (10952 voxels, peak = 89), gca=89.0 gca peak = 0.41356 (59) mri peak = 0.17326 (58) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (531 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (531 voxels, peak = 60), gca=60.5 gca peak = 0.59966 (56) mri peak = 0.15599 (57) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (609 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (609 voxels, peak = 56), gca=56.0 gca peak = 0.12277 (89) mri peak = 0.06726 (86) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4728 voxels, overlap=0.981) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4728 voxels, peak = 87), gca=86.8 gca peak = 0.11096 (81) mri peak = 0.06932 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4498 voxels, overlap=0.976) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4498 voxels, peak = 81), gca=81.0 gca peak = 0.09323 (78) mri peak = 0.07204 (72) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2693 voxels, overlap=0.910) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2693 voxels, peak = 78), gca=78.0 gca peak = 0.11778 (70) mri peak = 0.09590 (73) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2440 voxels, overlap=0.911) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2440 voxels, peak = 70), gca=70.0 gca peak = 0.07884 (86) mri peak = 0.07121 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13845 voxels, overlap=0.794) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13845 voxels, peak = 86), gca=86.0 gca peak = 0.12904 (91) mri peak = 0.10086 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1735 voxels, overlap=0.798) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1735 voxels, peak = 91), gca=91.0 gca peak = 0.15540 (90) mri peak = 0.08358 (94) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1998 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1998 voxels, peak = 92), gca=92.2 gca peak = 0.19579 (34) mri peak = 0.07330 (33) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (181 voxels, overlap=1.000) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (181 voxels, peak = 34), gca=34.0 gca peak = 0.27522 (18) mri peak = 0.21952 (15) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (931 voxels, overlap=0.835) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (931 voxels, peak = 14), gca=13.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24950 (33) gca peak CSF = 0.25719 (30) gca peak Left_Accumbens_area = 0.56657 (61) 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 = 0.23211 (29) gca peak Right_Accumbens_area = 0.32727 (70) gca peak Right_vessel = 0.77626 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (33) gca peak WM_hypointensities = 0.14094 (84) gca peak non_WM_hypointensities = 0.11940 (54) gca peak Optic_Chiasm = 0.34849 (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 0.94 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 14727 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels) 524 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 81718 changed. image ll: -2.137, PF=1.000 pass 2: 11376 changed. image ll: -2.137, PF=1.000 pass 3: 5058 changed. pass 4: 2669 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 19 minutes and 52 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/transforms/cc_up.lta avg35rerun will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/norm.mgz 34056 voxels in left wm, 38413 in right wm, xrange [123, 132] searching rotation angles z=[-3 11], y=[-7 7] 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 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.7 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.7 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.5 searching scale 1 Z rot 10.7 global minimum found at slice 127.3, rotations (-0.25, 3.99) final transformation (x=127.3, yr=-0.251, zr=3.989): 0.998 -0.070 -0.004 8.454; 0.070 0.998 -0.000 20.424; 0.004 -0.000 1.000 9.443; 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 128 149 172 eigenvectors: 0.001 0.003 1.000; 0.144 -0.990 0.003; 0.990 0.144 -0.001; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Tue Apr 20 15:02:48 EDT 2010 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Apr 20 15:02:49 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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... 3153 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 29 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 64 (64), valley at 0 (-1) csf peak at 32, setting threshold to 53 white matter peak found at 111 white matter peak found at 110 gm peak at 65 (65), valley at 0 (-1) csf peak at 32, setting threshold to 54 #-------------------------------------------- #@# Mask BFS Tue Apr 20 15:06:20 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1609501 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Apr 20 15:06:22 EDT 2010 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 (104.0): 103.7 +- 5.1 [80.0 --> 125.0] GM (74.0) : 73.4 +- 8.8 [30.0 --> 96.0] setting bottom of white matter range to 82.2 setting top of gray matter range to 91.0 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... 326 sparsely connected voxels removed... thickening thin strands.... 20 segments, 1907 filled 0 bright non-wm voxels segmented. 445 diagonally connected voxels added... white matter segmentation took 1.1 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 0.47 minutes reading wm segmentation from wm.seg.mgz... 138 voxels added to wm to prevent paths from MTL structures to cortex 1223 additional wm voxels added 0 additional wm voxels added SEG EDIT: 41324 voxels turned on, 89078 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+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 9 found - 9 modified | TOTAL: 23 pass 2 (xy-): 0 found - 9 modified | TOTAL: 23 pass 1 (yz+): 21 found - 21 modified | TOTAL: 44 pass 2 (yz+): 0 found - 21 modified | TOTAL: 44 pass 1 (yz-): 15 found - 15 modified | TOTAL: 59 pass 2 (yz-): 0 found - 15 modified | TOTAL: 59 pass 1 (xz+): 21 found - 21 modified | TOTAL: 80 pass 2 (xz+): 0 found - 21 modified | TOTAL: 80 pass 1 (xz-): 9 found - 9 modified | TOTAL: 89 pass 2 (xz-): 0 found - 9 modified | TOTAL: 89 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 Iteration Number : 1 pass 1 (++): 18 found - 18 modified | TOTAL: 18 pass 2 (++): 0 found - 18 modified | TOTAL: 18 pass 1 (+-): 19 found - 19 modified | TOTAL: 37 pass 2 (+-): 0 found - 19 modified | TOTAL: 37 pass 1 (--): 7 found - 7 modified | TOTAL: 44 pass 2 (--): 0 found - 7 modified | TOTAL: 44 pass 1 (-+): 22 found - 22 modified | TOTAL: 66 pass 2 (-+): 0 found - 22 modified | TOTAL: 66 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+): 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 : 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 (+-): 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 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 = 166 (out of 586859: 0.028286) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Apr 20 15:08:03 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 1.050 -0.107 0.003 2.714; 0.102 1.111 0.005 -16.960; -0.002 -0.005 0.951 -8.915; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.050 -0.107 0.003 2.714; 0.102 1.111 0.005 -16.960; -0.002 -0.005 0.951 -8.915; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1241 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max = 0.75) no need to search using seed (127, 122, 151), TAL = (1.0, 23.0, 6.0) talairach voxel to voxel transform 0.944 0.091 -0.004 -1.048; -0.087 0.891 -0.004 15.315; 0.002 0.005 1.051 9.457; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 122, 151) --> (1.0, 23.0, 6.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (1.00, 23.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 23.00, 6.00) SRC: (112.39, 113.97, 169.04) search lh wm seed point around talairach space (-17.00, 23.00, 6.00), SRC: (146.36, 110.85, 169.10) 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 Apr 20 15:08:59 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 (-+): 0 found - 0 modified | TOTAL: 0 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 = 2 (out of 289805: 0.000690) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ slice 50: 3053 vertices, 3231 faces slice 60: 10585 vertices, 10859 faces slice 70: 18430 vertices, 18696 faces slice 80: 27972 vertices, 28306 faces slice 90: 38346 vertices, 38719 faces slice 100: 47858 vertices, 48189 faces slice 110: 59702 vertices, 60089 faces slice 120: 71458 vertices, 71874 faces slice 130: 83043 vertices, 83456 faces slice 140: 93740 vertices, 94084 faces slice 150: 103830 vertices, 104167 faces slice 160: 112195 vertices, 112469 faces slice 170: 119832 vertices, 120100 faces slice 180: 126656 vertices, 126875 faces slice 190: 132861 vertices, 133052 faces slice 200: 137532 vertices, 137669 faces slice 210: 140482 vertices, 140539 faces slice 220: 140700 vertices, 140706 faces slice 230: 140700 vertices, 140706 faces slice 240: 140700 vertices, 140706 faces slice 250: 140700 vertices, 140706 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... 140700 voxel in cpt #1: X=-6 [v=140700,e=422118,f=281412] located at (-26.979887, -8.392189, 25.932743) For the whole surface: X=-6 [v=140700,e=422118,f=281412] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Apr 20 15:09:09 EDT 2010 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 Apr 20 15:09:14 EDT 2010 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts avg radius = 48.8 mm, total surface area = 76367 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.094 (target=0.015) step 005: RMS=0.070 (target=0.015) step 010: RMS=0.050 (target=0.015) step 015: RMS=0.041 (target=0.015) step 020: RMS=0.035 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.020 (target=0.015) step 050: RMS=0.020 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Apr 20 15:10:13 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.57 (0.00-->7.30) (max @ vno 101412 --> 102542) face area 0.02 +- 0.03 (-0.05-->0.61) scaling brain by 0.296... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.067, avgs=0 005/300: dt: 0.9000, rms radial error=176.808, avgs=0 010/300: dt: 0.9000, rms radial error=176.253, avgs=0 015/300: dt: 0.9000, rms radial error=175.523, avgs=0 020/300: dt: 0.9000, rms radial error=174.691, avgs=0 025/300: dt: 0.9000, rms radial error=173.801, avgs=0 030/300: dt: 0.9000, rms radial error=172.879, avgs=0 035/300: dt: 0.9000, rms radial error=171.940, avgs=0 040/300: dt: 0.9000, rms radial error=170.994, avgs=0 045/300: dt: 0.9000, rms radial error=170.045, avgs=0 050/300: dt: 0.9000, rms radial error=169.097, avgs=0 055/300: dt: 0.9000, rms radial error=168.151, avgs=0 060/300: dt: 0.9000, rms radial error=167.209, avgs=0 065/300: dt: 0.9000, rms radial error=166.271, avgs=0 070/300: dt: 0.9000, rms radial error=165.337, avgs=0 075/300: dt: 0.9000, rms radial error=164.408, avgs=0 080/300: dt: 0.9000, rms radial error=163.484, avgs=0 085/300: dt: 0.9000, rms radial error=162.564, avgs=0 090/300: dt: 0.9000, rms radial error=161.650, avgs=0 095/300: dt: 0.9000, rms radial error=160.740, avgs=0 100/300: dt: 0.9000, rms radial error=159.835, avgs=0 105/300: dt: 0.9000, rms radial error=158.934, avgs=0 110/300: dt: 0.9000, rms radial error=158.039, avgs=0 115/300: dt: 0.9000, rms radial error=157.148, avgs=0 120/300: dt: 0.9000, rms radial error=156.262, avgs=0 125/300: dt: 0.9000, rms radial error=155.381, avgs=0 130/300: dt: 0.9000, rms radial error=154.505, avgs=0 135/300: dt: 0.9000, rms radial error=153.634, avgs=0 140/300: dt: 0.9000, rms radial error=152.768, avgs=0 145/300: dt: 0.9000, rms radial error=151.906, avgs=0 150/300: dt: 0.9000, rms radial error=151.050, avgs=0 155/300: dt: 0.9000, rms radial error=150.198, avgs=0 160/300: dt: 0.9000, rms radial error=149.351, avgs=0 165/300: dt: 0.9000, rms radial error=148.508, avgs=0 170/300: dt: 0.9000, rms radial error=147.671, avgs=0 175/300: dt: 0.9000, rms radial error=146.840, avgs=0 180/300: dt: 0.9000, rms radial error=146.014, avgs=0 185/300: dt: 0.9000, rms radial error=145.192, avgs=0 190/300: dt: 0.9000, rms radial error=144.375, avgs=0 195/300: dt: 0.9000, rms radial error=143.563, avgs=0 200/300: dt: 0.9000, rms radial error=142.755, avgs=0 205/300: dt: 0.9000, rms radial error=141.951, avgs=0 210/300: dt: 0.9000, rms radial error=141.152, avgs=0 215/300: dt: 0.9000, rms radial error=140.358, avgs=0 220/300: dt: 0.9000, rms radial error=139.567, avgs=0 225/300: dt: 0.9000, rms radial error=138.781, avgs=0 230/300: dt: 0.9000, rms radial error=138.000, avgs=0 235/300: dt: 0.9000, rms radial error=137.223, avgs=0 240/300: dt: 0.9000, rms radial error=136.450, avgs=0 245/300: dt: 0.9000, rms radial error=135.681, avgs=0 250/300: dt: 0.9000, rms radial error=134.917, avgs=0 255/300: dt: 0.9000, rms radial error=134.157, avgs=0 260/300: dt: 0.9000, rms radial error=133.401, avgs=0 265/300: dt: 0.9000, rms radial error=132.649, avgs=0 270/300: dt: 0.9000, rms radial error=131.902, avgs=0 275/300: dt: 0.9000, rms radial error=131.159, avgs=0 280/300: dt: 0.9000, rms radial error=130.420, avgs=0 285/300: dt: 0.9000, rms radial error=129.685, avgs=0 290/300: dt: 0.9000, rms radial error=128.954, avgs=0 295/300: dt: 0.9000, rms radial error=128.228, avgs=0 300/300: dt: 0.9000, rms radial error=127.505, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 7252.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 2 (K=80.0), pass 1, starting sse = 992.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00077 epoch 3 (K=320.0), pass 1, starting sse = 75.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/14 = 0.01439 epoch 4 (K=1280.0), pass 1, starting sse = 3.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.26/18 = 0.01425 final diswriting spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.11 hours tance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Apr 20 15:17:06 EDT 2010 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 avg35rerun 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 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ before topology correction, eno=-6 (nv=140700, nf=281412, ne=422118, g=4) 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 13 iterations marking ambiguous vertices... 2723 ambiguous faces found in tessellation segmenting defects... 7 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 7 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1221 (-4.5611) -vertex loglikelihood: -5.9679 (-2.9840) -normal dot loglikelihood: -3.5908 (-3.5908) -quad curv loglikelihood: -6.3840 (-3.1920) Total Loglikelihood : -25.0648 CORRECTING DEFECT 0 (vertices=186, convex hull=96) After retessellation of defect 0, euler #=-4 (139226,417462,278232) : difference with theory (-4) = 0 CORRECTING DEFECT 1 (vertices=96, convex hull=67) After retessellation of defect 1, euler #=-3 (139239,417529,278287) : difference with theory (-3) = 0 CORRECTING DEFECT 2 (vertices=106, convex hull=105) After retessellation of defect 2, euler #=-2 (139284,417709,278423) : difference with theory (-2) = 0 CORRECTING DEFECT 3 (vertices=12, convex hull=13) After retessellation of defect 3, euler #=-1 (139286,417717,278430) : difference with theory (-1) = 0 CORRECTING DEFECT 4 (vertices=45, convex hull=71) After retessellation of defect 4, euler #=0 (139305,417803,278498) : difference with theory (0) = 0 CORRECTING DEFECT 5 (vertices=954, convex hull=104) After retessellation of defect 5, euler #=1 (139315,417882,278568) : difference with theory (1) = 0 CORRECTING DEFECT 6 (vertices=97, convex hull=128) After retessellation of defect 6, euler #=2 (139336,418002,278668) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.14-->17.01) (max @ vno 96952 --> 107761) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.14-->17.01) (max @ vno 96952 --> 107761) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 31 mutations (31.6%), 67 crossovers (68.4%), 148 vertices were eliminated building final representation... 1364 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139336, nf=278668, ne=418002, g=0) writing corrected surface to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.4 minutes 0 defective edges removing intersecting faces 000: 93 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 139336 - 418002 + 278668 = 2 --> 0 holes F =2V-4: 278668 = 278672-4 (0) 2E=3F: 836004 = 836004 (0) total defect index = 0 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 7 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make Final Surf lh Tue Apr 20 15:28:40 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs avg35rerun lh 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 1.113 2010/04/08 19:42:02 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/filled.mgz... reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... 12424 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.orig... computing class statistics... border white: 258602 voxels (1.54%) border gray 281737 voxels (1.68%) WM (99.0): 98.9 +- 7.4 [70.0 --> 110.0] GM (76.0) : 75.1 +- 9.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.7 (was 70) setting MAX_BORDER_WHITE to 109.4 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 52.5 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.03-->3.23) (max @ vno 94942 --> 96952) face area 0.29 +- 0.12 (0.00-->2.33) mean absolute distance = 0.72 +- 0.87 3758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=71 using class modes intead of means.... mean inside = 94.7, mean outside = 78.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=81.7, 62 (62) missing vertices, mean dist 0.3 [0.5 (%35.0)->0.8 (%65.0))] %67 local maxima, %28 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 +- 0.25 (0.14-->3.85) (max @ vno 106815 --> 106820) face area 0.29 +- 0.13 (0.00-->2.28) mean absolute distance = 0.32 +- 0.68 1795 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4698743.0, rms=9.63 001: dt: 0.5000, sse=5003703.0, rms=7.01 002: dt: 0.5000, sse=5190080.0, rms=5.37 003: dt: 0.5000, sse=5387696.5, rms=4.28 004: dt: 0.5000, sse=5499223.5, rms=3.54 005: dt: 0.5000, sse=5593432.0, rms=3.15 006: dt: 0.5000, sse=5638879.5, rms=2.91 007: dt: 0.5000, sse=5676985.0, rms=2.82 008: dt: 0.5000, sse=5671074.5, rms=2.74 rms = 2.74, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5676244.0, rms=2.74 010: dt: 0.2500, sse=3095319.0, rms=1.63 011: dt: 0.2500, sse=2807395.8, rms=1.39 012: dt: 0.2500, sse=2700168.0, rms=1.34 rms = 1.31, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=2667730.5, rms=1.31 rms = 1.29, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=2633276.8, rms=1.29 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 12 (2) missing vertices, mean dist -0.2 [0.4 (%68.7)->0.2 (%31.3))] %72 local maxima, %23 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 0.93 +- 0.24 (0.13-->3.35) (max @ vno 94797 --> 94801) face area 0.36 +- 0.16 (0.00-->2.90) mean absolute distance = 0.26 +- 0.46 2630 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3068688.2, rms=3.60 015: dt: 0.5000, sse=3321339.0, rms=2.11 rms = 2.12, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=3107464.8, rms=1.65 017: dt: 0.2500, sse=3029930.2, rms=1.29 018: dt: 0.2500, sse=2974685.0, rms=1.16 rms = 1.12, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=2951949.8, rms=1.12 rms = 1.10, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=2927322.8, rms=1.10 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.9, 7 (0) missing vertices, mean dist -0.1 [0.3 (%72.7)->0.2 (%27.3))] %81 local maxima, %13 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 0.92 +- 0.24 (0.09-->3.44) (max @ vno 94797 --> 94801) face area 0.36 +- 0.16 (0.00-->2.92) mean absolute distance = 0.22 +- 0.34 3079 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3126438.5, rms=3.01 021: dt: 0.5000, sse=3451766.0, rms=2.03 rms = 2.20, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=3270091.5, rms=1.49 023: dt: 0.2500, sse=3185848.5, rms=1.17 024: dt: 0.2500, sse=3151125.2, rms=1.07 rms = 1.05, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3134336.0, rms=1.05 rms = 1.04, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3118783.0, rms=1.04 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.8, 9 (0) missing vertices, mean dist -0.1 [0.2 (%60.3)->0.2 (%39.7))] %87 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3155502.2, rms=1.73 027: dt: 0.5000, sse=3845522.8, rms=1.31 rms = 1.68, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3548311.8, rms=1.01 029: dt: 0.2500, sse=3406075.2, rms=0.92 rms = 0.88, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3443051.5, rms=0.88 rms = 0.87, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3446501.5, rms=0.87 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... label Left_Amygdala: removing 1 voxels in segment 1 generating cortex label... 16 non-cortical segments detected only using segment with 1895 vertices erasing segment 1 (vno[0] = 56738) erasing segment 2 (vno[0] = 72187) erasing segment 3 (vno[0] = 79969) erasing segment 4 (vno[0] = 82230) erasing segment 5 (vno[0] = 84652) erasing segment 6 (vno[0] = 87895) erasing segment 7 (vno[0] = 89965) erasing segment 8 (vno[0] = 92023) erasing segment 9 (vno[0] = 96878) erasing segment 10 (vno[0] = 99574) erasing segment 11 (vno[0] = 100556) erasing segment 12 (vno[0] = 106864) erasing segment 13 (vno[0] = 108418) erasing segment 14 (vno[0] = 108499) erasing segment 15 (vno[0] = 109206) writing cortex label to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label/lh.cortex.label... LabelWrite: saving to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label/lh.cortex.label writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.area vertex spacing 0.91 +- 0.24 (0.11-->3.85) (max @ vno 106820 --> 106815) face area 0.35 +- 0.15 (0.00-->2.91) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=62.7, 15 (15) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.2 (%100.0))] %16 local maxima, %57 large gradients and %23 min vals, 1686 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=18965982.0, rms=24.79 001: dt: 0.5000, sse=14523216.0, rms=21.21 002: dt: 0.5000, sse=11271098.0, rms=18.19 003: dt: 0.5000, sse=9031024.0, rms=15.65 004: dt: 0.5000, sse=7518662.5, rms=13.42 005: dt: 0.5000, sse=6428902.0, rms=11.49 006: dt: 0.5000, sse=5622292.0, rms=9.85 007: dt: 0.5000, sse=5071193.0, rms=8.42 008: dt: 0.5000, sse=4667426.5, rms=7.16 009: dt: 0.5000, sse=4399260.5, rms=6.06 010: dt: 0.5000, sse=4215063.5, rms=5.10 011: dt: 0.5000, sse=4119747.2, rms=4.32 012: dt: 0.5000, sse=4067891.2, rms=3.71 013: dt: 0.5000, sse=4061521.0, rms=3.25 014: dt: 0.5000, sse=4055391.0, rms=2.91 015: dt: 0.5000, sse=4062778.2, rms=2.66 016: dt: 0.5000, sse=4075948.8, rms=2.49 017: dt: 0.5000, sse=4075794.8, rms=2.38 018: dt: 0.5000, sse=4086054.0, rms=2.31 019: dt: 0.5000, sse=4067787.0, rms=2.25 rms = 2.21, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=4068012.5, rms=2.21 021: dt: 0.2500, sse=2949076.2, rms=1.73 022: dt: 0.2500, sse=2845492.8, rms=1.62 rms = 1.59, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2805532.0, rms=1.59 rms = 1.56, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=2746113.8, rms=1.56 positioning took 2.6 minutes mean border=61.3, 796 (0) missing vertices, mean dist 0.2 [0.2 (%55.2)->0.7 (%44.8))] %28 local maxima, %50 large gradients and %17 min vals, 763 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=3168631.0, rms=3.31 025: dt: 0.5000, sse=3427881.5, rms=2.49 026: dt: 0.5000, sse=3839504.0, rms=2.22 027: dt: 0.5000, sse=4002406.0, rms=2.13 rms = 2.13, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=4172592.8, rms=2.13 029: dt: 0.2500, sse=3311540.5, rms=1.62 030: dt: 0.2500, sse=3224529.5, rms=1.52 rms = 1.50, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=3189038.5, rms=1.50 rms = 1.46, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3130842.8, rms=1.46 positioning took 0.9 minutes mean border=60.4, 1409 (0) missing vertices, mean dist 0.1 [0.2 (%51.8)->0.5 (%48.2))] %42 local maxima, %36 large gradients and %16 min vals, 637 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=3240594.2, rms=2.30 033: dt: 0.5000, sse=3456401.0, rms=1.85 rms = 1.85, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=3857737.0, rms=1.85 035: dt: 0.2500, sse=3362084.0, rms=1.43 036: dt: 0.2500, sse=3313378.0, rms=1.36 rms = 1.35, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=3296242.2, rms=1.35 rms = 1.31, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3243047.2, rms=1.31 positioning took 0.6 minutes mean border=59.5, 2804 (0) missing vertices, mean dist 0.1 [0.2 (%47.2)->0.5 (%52.8))] %54 local maxima, %24 large gradients and %15 min vals, 634 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3294908.2, rms=1.89 039: dt: 0.5000, sse=3418234.8, rms=1.58 rms = 1.60, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=3286092.8, rms=1.36 041: dt: 0.2500, sse=3262854.0, rms=1.23 rms = 1.21, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=3262460.8, rms=1.21 rms = 1.18, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=3214919.2, rms=1.18 positioning took 0.6 minutes writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.area.pial vertex spacing 1.00 +- 0.40 (0.09-->8.12) (max @ vno 105999 --> 105994) face area 0.41 +- 0.28 (0.00-->5.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 139336 vertices processed 25000 of 139336 vertices processed 50000 of 139336 vertices processed 75000 of 139336 vertices processed 100000 of 139336 vertices processed 125000 of 139336 vertices processed 0 of 139336 vertices processed 25000 of 139336 vertices processed 50000 of 139336 vertices processed 75000 of 139336 vertices processed 100000 of 139336 vertices processed 125000 of 139336 vertices processed thickness calculation complete, 1710:1644 truncations. 69206 vertices at 0 distance 91548 vertices at 1 distance 64397 vertices at 2 distance 25627 vertices at 3 distance 9616 vertices at 4 distance 3493 vertices at 5 distance 1284 vertices at 6 distance 541 vertices at 7 distance 307 vertices at 8 distance 175 vertices at 9 distance 97 vertices at 10 distance 64 vertices at 11 distance 49 vertices at 12 distance 35 vertices at 13 distance 28 vertices at 14 distance 31 vertices at 15 distance 31 vertices at 16 distance 24 vertices at 17 distance 32 vertices at 18 distance 11 vertices at 19 distance 24 vertices at 20 distance writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.thickness positioning took 14.4 minutes #-------------------------------------------- #@# Surf Volume lh Tue Apr 20 15:43:03 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc -o lh.volume lh.area.mid mul lh.thickness #-------------------------------------------- #@# Smooth2 lh Tue Apr 20 15:43:04 EDT 2010 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 Apr 20 15:43:09 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 49.0 mm, total surface area = 88723 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.110 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (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/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 289 vertices thresholded to be in k1 ~ [-0.22 0.29], k2 ~ [-0.09 0.05] total integrated curvature = 0.532*4pi (6.687) --> 0 handles ICI = 1.8, FI = 11.9, variation=202.621 154 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 = 0.001 163 vertices thresholded to be in [-0.13 0.15] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Tue Apr 20 15:45:35 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm avg35rerun 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 [ avg35rerun/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 225 ] WARN: S lookup min: -0.502306 WARN: S explicit min: 0.000000 vertex = 262 #-------------------------------------------- #@# Sphere lh Tue Apr 20 15:45:42 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 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 1.45 hours scaling brain by 0.275... pass 1: epoch 1 of 3 starting distance error %20.69 pass 1: epoch 2 of 3 starting distance error %20.67 unfolding complete - removing small folds... starting distance error %20.61 removing remaining folds... final distance error %20.61 304: 0 negative triangles #-------------------------------------------- #@# Surf Reg lh Tue Apr 20 17:12:59 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.591 curvature mean = 0.039, std = 0.929 curvature mean = 0.012, std = 0.848 curvature mean = 0.018, std = 0.950 curvature mean = 0.006, std = 0.937 curvature mean = 0.014, std = 0.959 curvature mean = 0.002, std = 0.972 curvature mean = 0.011, std = 0.960 curvature mean = 0.001, std = 0.988 curvature mean = -0.021, std = 0.263 curvature mean = 0.004, std = 0.067 curvature mean = 0.038, std = 0.387 curvature mean = 0.004, std = 0.080 curvature mean = 0.018, std = 0.584 curvature mean = 0.004, std = 0.086 curvature mean = 0.008, std = 0.720 curvature mean = 0.004, std = 0.088 curvature mean = 0.002, std = 0.808 146: 0 negative triangles #-------------------------------------------- #@# Jacobian white lh Tue Apr 20 18:04:26 EDT 2010 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 Apr 20 18:04:29 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev/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/dev/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Apr 20 18:04:32 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 avg35rerun lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/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 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 1301 labels changed using aseg relabeling using gibbs priors... 000: 3017 changed, 139336 examined... 001: 728 changed, 13007 examined... 002: 195 changed, 3930 examined... 003: 61 changed, 1185 examined... 004: 15 changed, 359 examined... 005: 8 changed, 105 examined... 006: 2 changed, 45 examined... 007: 0 changed, 14 examined... 230 labels changed using aseg 000: 105 total segments, 58 labels (162 vertices) changed 001: 47 total segments, 3 labels (12 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1648 vertices marked for relabeling... 1648 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 54 seconds. #----------------------------------------- #@# Parcellation Stats lh Tue Apr 20 18:05:26 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 avg35rerun lh computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert and SurfArea. 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 1604 1093 2463 2.294 0.644 0.094 0.020 8 1.3 bankssts 1025 678 1970 2.644 0.827 0.147 0.039 16 1.5 caudalanteriorcingulate 4151 2823 6297 2.017 0.552 0.121 0.027 34 4.7 caudalmiddlefrontal 2160 1552 3340 2.124 0.547 0.152 0.042 25 3.6 cuneus 719 478 2325 3.564 0.860 0.120 0.033 5 1.1 entorhinal 5720 4068 11526 2.701 0.629 0.143 0.041 67 9.0 fusiform 7032 4872 12491 2.252 0.699 0.130 0.035 68 9.7 inferiorparietal 6171 4383 13751 2.809 0.814 0.139 0.039 71 10.0 inferiortemporal 1505 1022 2751 2.521 0.873 0.134 0.041 19 2.4 isthmuscingulate 7934 5594 13087 2.317 0.615 0.145 0.044 101 14.1 lateraloccipital 3830 2631 7520 2.535 0.923 0.134 0.038 45 5.6 lateralorbitofrontal 5030 3608 8332 2.238 0.643 0.144 0.043 59 8.4 lingual 2929 2207 6104 2.483 0.955 0.138 0.147 71 29.7 medialorbitofrontal 4858 3358 11189 2.733 0.849 0.119 0.028 45 5.6 middletemporal 1248 816 2099 2.246 0.630 0.078 0.014 5 0.7 parahippocampal 1813 1223 2471 1.899 0.541 0.122 0.027 14 2.0 paracentral 2192 1551 3811 2.027 0.627 0.126 0.032 25 2.8 parsopercularis 1039 718 2056 2.327 0.824 0.162 0.050 18 2.1 parsorbitalis 1921 1384 3837 2.259 0.734 0.149 0.041 25 3.2 parstriangularis 1850 1309 2116 1.909 0.502 0.151 0.049 30 3.8 pericalcarine 7621 5087 9889 1.775 0.627 0.117 0.028 61 8.6 postcentral 1724 1173 2461 2.035 0.976 0.140 0.037 25 2.5 posteriorcingulate 8328 5413 12082 2.060 0.633 0.114 0.027 64 9.3 precentral 5410 3782 8938 2.181 0.617 0.134 0.036 56 8.0 precuneus 1210 810 2272 2.473 0.955 0.147 0.144 70 4.3 rostralanteriorcingulate 7544 5413 12871 1.993 0.727 0.152 0.052 111 15.1 rostralmiddlefrontal 10710 7419 21102 2.358 0.875 0.130 0.035 110 14.9 superiorfrontal 8327 5694 12010 1.966 0.565 0.130 0.031 78 10.6 superiorparietal 5466 3662 9949 2.438 0.748 0.104 0.022 40 5.2 superiortemporal 5158 3655 9598 2.408 0.738 0.139 0.038 57 7.5 supramarginal 326 236 760 2.425 0.565 0.194 0.079 7 1.1 frontalpole 700 492 2849 4.053 0.555 0.134 0.042 8 1.2 temporalpole 609 408 982 2.349 0.540 0.131 0.032 6 0.7 transversetemporal 3364 2268 6838 2.933 1.168 0.097 0.031 60 3.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Apr 20 18:05:42 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 avg35rerun lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/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 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 91 labels changed using aseg relabeling using gibbs priors... 000: 9486 changed, 139336 examined... 001: 2292 changed, 35860 examined... 002: 690 changed, 11609 examined... 003: 287 changed, 3828 examined... 004: 155 changed, 1660 examined... 005: 89 changed, 873 examined... 006: 63 changed, 495 examined... 007: 26 changed, 312 examined... 008: 18 changed, 159 examined... 009: 7 changed, 89 examined... 010: 2 changed, 46 examined... 011: 0 changed, 11 examined... 14 labels changed using aseg 000: 278 total segments, 198 labels (2488 vertices) changed 001: 96 total segments, 16 labels (38 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 129 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1001 vertices marked for relabeling... 1001 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 1 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Apr 20 18:06:43 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 avg35rerun lh computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert and SurfArea. 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 1180 841 2055 2.091 0.642 0.159 0.056 22 2.7 G_and_S_frontomargin 1963 1391 3278 2.379 0.639 0.151 0.042 24 3.3 G_and_S_occipital_inf 1511 978 2039 1.834 0.510 0.121 0.030 14 1.7 G_and_S_paracentral 1512 1046 3251 2.519 0.741 0.138 0.035 19 2.1 G_and_S_subcentral 617 479 1545 2.539 0.504 0.200 0.089 16 1.9 G_and_S_transv_frontopol 2591 1815 4993 2.334 0.971 0.144 0.043 37 4.0 G_and_S_cingul-Ant 1356 950 2097 2.035 0.715 0.125 0.027 13 1.6 G_and_S_cingul-Mid-Ant 1464 1007 1974 1.835 0.531 0.131 0.035 18 1.9 G_and_S_cingul-Mid-Post 459 336 1240 3.276 0.769 0.196 0.077 10 1.4 G_cingul-Post-dorsal 356 225 603 2.442 0.961 0.135 0.039 5 0.5 G_cingul-Post-ventral 1943 1420 3080 2.056 0.575 0.165 0.048 26 3.7 G_cuneus 1359 976 3098 2.445 0.636 0.147 0.039 22 2.1 G_front_inf-Opercular 308 206 649 2.410 0.791 0.179 0.059 6 0.6 G_front_inf-Orbital 1000 726 2486 2.493 0.725 0.169 0.050 17 2.2 G_front_inf-Triangul 4601 3298 9723 2.282 0.677 0.153 0.049 66 8.7 G_front_middle 7083 4877 16395 2.659 0.805 0.138 0.039 82 11.2 G_front_sup 462 303 1288 3.743 1.026 0.119 0.066 41 0.6 G_Ins_lg_and_S_cent_ins 643 422 2048 3.641 0.911 0.104 0.044 8 0.7 G_insular_short 2325 1610 5134 2.540 0.582 0.146 0.040 29 3.7 G_occipital_middle 1708 1228 3027 2.373 0.526 0.166 0.047 24 3.2 G_occipital_sup 2342 1650 4998 2.569 0.535 0.146 0.044 32 3.9 G_oc-temp_lat-fusifor 3051 2213 5620 2.241 0.678 0.153 0.047 41 5.8 G_oc-temp_med-Lingual 1319 867 3444 3.021 0.980 0.096 0.021 7 1.1 G_oc-temp_med-Parahip 2631 1806 6319 2.722 0.838 0.157 0.049 47 5.1 G_orbital 2510 1805 5938 2.680 0.650 0.162 0.055 37 4.9 G_pariet_inf-Angular 3004 2148 6457 2.593 0.696 0.151 0.043 39 5.0 G_pariet_inf-Supramar 2962 2015 5263 2.162 0.565 0.136 0.034 31 4.2 G_parietal_sup 3341 2169 4224 1.773 0.525 0.115 0.027 24 3.7 G_postcentral 2898 1781 4751 2.200 0.578 0.108 0.029 20 3.5 G_precentral 2573 1834 5358 2.414 0.601 0.149 0.042 35 4.5 G_precuneus 1083 869 2656 2.315 0.765 0.168 0.055 21 2.5 G_rectus 410 291 842 2.867 0.765 0.153 0.359 58 3.4 G_subcallosal 399 248 646 2.187 0.405 0.128 0.034 4 0.5 G_temp_sup-G_T_transv 2062 1371 5023 2.697 0.668 0.132 0.033 25 2.9 G_temp_sup-Lateral 760 523 1789 3.181 0.945 0.065 0.012 2 0.3 G_temp_sup-Plan_polar 859 610 1486 2.261 0.601 0.101 0.023 5 0.8 G_temp_sup-Plan_tempo 3395 2435 9333 3.047 0.784 0.157 0.049 50 7.0 G_temporal_inf 2927 2008 8394 3.074 0.734 0.129 0.033 34 3.9 G_temporal_middle 386 272 696 2.292 0.504 0.142 0.038 5 0.6 Lat_Fis-ant-Horizont 256 178 417 2.160 0.790 0.115 0.029 2 0.2 Lat_Fis-ant-Vertical 1257 824 1532 2.172 0.793 0.099 0.021 6 1.1 Lat_Fis-post 2182 1537 3909 2.261 0.799 0.148 0.056 40 4.9 Pole_occipital 1762 1250 6046 3.519 0.896 0.145 0.044 21 3.3 Pole_temporal 2398 1664 2906 1.987 0.574 0.133 0.048 31 4.3 S_calcarine 3323 2189 3008 1.505 0.507 0.106 0.023 21 3.2 S_central 1103 732 1322 1.727 0.790 0.109 0.025 7 1.3 S_cingul-Marginalis 594 395 798 2.104 0.466 0.092 0.018 2 0.5 S_circular_insula_ant 1482 1003 2248 2.525 1.010 0.075 0.011 4 0.7 S_circular_insula_inf 1962 1354 2223 1.825 0.557 0.095 0.019 10 1.5 S_circular_insula_sup 902 684 2021 3.165 0.941 0.148 0.041 9 1.4 S_collat_transv_ant 660 444 721 1.968 0.357 0.147 0.038 8 1.1 S_collat_transv_post 2245 1544 2417 1.576 0.423 0.123 0.034 20 2.9 S_front_inf 1250 878 1561 1.713 0.645 0.126 0.033 10 1.7 S_front_middle 2999 2082 3592 1.727 0.592 0.114 0.026 21 3.3 S_front_sup 287 202 353 2.083 0.773 0.121 0.026 2 0.3 S_interm_prim-Jensen 2928 1990 3247 1.746 0.434 0.117 0.027 22 3.3 S_intrapariet_and_P_trans 1072 781 1405 2.264 0.415 0.146 0.040 10 1.7 S_oc_middle_and_Lunatus 1387 955 1699 2.067 0.508 0.108 0.026 7 1.5 S_oc_sup_and_transversal 1173 811 1531 2.320 0.454 0.107 0.025 7 1.2 S_occipital_ant 1174 799 1627 2.581 0.473 0.133 0.036 12 1.7 S_oc-temp_lat 3081 2154 4418 2.426 0.574 0.119 0.027 24 3.6 S_oc-temp_med_and_Lingual 438 295 496 1.709 0.516 0.114 0.029 2 0.5 S_orbital_lateral 990 708 1850 2.754 1.299 0.112 0.338 38 25.8 S_orbital_med-olfact 1295 917 2060 2.298 0.979 0.134 0.037 12 2.0 S_orbital-H_Shaped 1807 1280 2468 2.033 0.548 0.123 0.028 14 2.0 S_parieto_occipital 1280 797 1422 2.271 0.873 0.118 0.024 17 1.2 S_pericallosal 3614 2464 4274 1.804 0.534 0.115 0.025 26 3.7 S_postcentral 1433 1000 1941 1.918 0.450 0.126 0.029 13 1.6 S_precentral-inf-part 1635 1111 1859 1.931 0.430 0.105 0.020 9 1.5 S_precentral-sup-part 560 423 1005 2.394 0.681 0.118 0.027 4 0.6 S_suborbital 1171 800 1416 1.854 0.505 0.122 0.031 9 1.3 S_subparietal 2172 1534 3072 2.252 0.588 0.106 0.021 13 1.9 S_temporal_inf 5569 3762 7338 2.030 0.582 0.099 0.020 29 4.6 S_temporal_sup 434 296 694 2.904 0.709 0.137 0.027 5 0.5 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Tue Apr 20 18:07:02 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 (-+): 0 found - 0 modified | TOTAL: 0 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 = 1 (out of 276122: 0.000362) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ slice 50: 1761 vertices, 1871 faces slice 60: 6746 vertices, 6972 faces slice 70: 14390 vertices, 14684 faces slice 80: 23626 vertices, 23978 faces slice 90: 34302 vertices, 34636 faces slice 100: 44421 vertices, 44748 faces slice 110: 55537 vertices, 55908 faces slice 120: 67110 vertices, 67475 faces slice 130: 78226 vertices, 78612 faces slice 140: 89336 vertices, 89707 faces slice 150: 99866 vertices, 100240 faces slice 160: 108265 vertices, 108525 faces slice 170: 115547 vertices, 115799 faces slice 180: 122155 vertices, 122404 faces slice 190: 128223 vertices, 128435 faces slice 200: 133078 vertices, 133226 faces slice 210: 136076 vertices, 136135 faces slice 220: 136216 vertices, 136224 faces slice 230: 136216 vertices, 136224 faces slice 240: 136216 vertices, 136224 faces slice 250: 136216 vertices, 136224 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... 136216 voxel in cpt #1: X=-8 [v=136216,e=408672,f=272448] located at (27.079176, -6.355935, 22.052513) For the whole surface: X=-8 [v=136216,e=408672,f=272448] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Apr 20 18:07:11 EDT 2010 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 Apr 20 18:07:16 EDT 2010 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts avg radius = 47.5 mm, total surface area = 74284 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.093 (target=0.015) step 005: RMS=0.069 (target=0.015) step 010: RMS=0.050 (target=0.015) step 015: RMS=0.042 (target=0.015) step 020: RMS=0.036 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Apr 20 18:08:13 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.56 (0.00-->7.06) (max @ vno 46068 --> 47079) face area 0.02 +- 0.03 (-0.14-->0.58) scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.249, avgs=0 005/300: dt: 0.9000, rms radial error=176.989, avgs=0 010/300: dt: 0.9000, rms radial error=176.433, avgs=0 015/300: dt: 0.9000, rms radial error=175.702, avgs=0 020/300: dt: 0.9000, rms radial error=174.869, avgs=0 025/300: dt: 0.9000, rms radial error=173.979, avgs=0 030/300: dt: 0.9000, rms radial error=173.055, avgs=0 035/300: dt: 0.9000, rms radial error=172.116, avgs=0 040/300: dt: 0.9000, rms radial error=171.168, avgs=0 045/300: dt: 0.9000, rms radial error=170.219, avgs=0 050/300: dt: 0.9000, rms radial error=169.271, avgs=0 055/300: dt: 0.9000, rms radial error=168.326, avgs=0 060/300: dt: 0.9000, rms radial error=167.385, avgs=0 065/300: dt: 0.9000, rms radial error=166.448, avgs=0 070/300: dt: 0.9000, rms radial error=165.516, avgs=0 075/300: dt: 0.9000, rms radial error=164.590, avgs=0 080/300: dt: 0.9000, rms radial error=163.668, avgs=0 085/300: dt: 0.9000, rms radial error=162.752, avgs=0 090/300: dt: 0.9000, rms radial error=161.841, avgs=0 095/300: dt: 0.9000, rms radial error=160.934, avgs=0 100/300: dt: 0.9000, rms radial error=160.033, avgs=0 105/300: dt: 0.9000, rms radial error=159.136, avgs=0 110/300: dt: 0.9000, rms radial error=158.245, avgs=0 115/300: dt: 0.9000, rms radial error=157.358, avgs=0 120/300: dt: 0.9000, rms radial error=156.476, avgs=0 125/300: dt: 0.9000, rms radial error=155.598, avgs=0 130/300: dt: 0.9000, rms radial error=154.726, avgs=0 135/300: dt: 0.9000, rms radial error=153.858, avgs=0 140/300: dt: 0.9000, rms radial error=152.994, avgs=0 145/300: dt: 0.9000, rms radial error=152.136, avgs=0 150/300: dt: 0.9000, rms radial error=151.282, avgs=0 155/300: dt: 0.9000, rms radial error=150.433, avgs=0 160/300: dt: 0.9000, rms radial error=149.588, avgs=0 165/300: dt: 0.9000, rms radial error=148.748, avgs=0 170/300: dt: 0.9000, rms radial error=147.912, avgs=0 175/300: dt: 0.9000, rms radial error=147.081, avgs=0 180/300: dt: 0.9000, rms radial error=146.255, avgs=0 185/300: dt: 0.9000, rms radial error=145.433, avgs=0 190/300: dt: 0.9000, rms radial error=144.616, avgs=0 195/300: dt: 0.9000, rms radial error=143.803, avgs=0 200/300: dt: 0.9000, rms radial error=142.995, avgs=0 205/300: dt: 0.9000, rms radial error=142.191, avgs=0 210/300: dt: 0.9000, rms radial error=141.391, avgs=0 215/300: dt: 0.9000, rms radial error=140.596, avgs=0 220/300: dt: 0.9000, rms radial error=139.805, avgs=0 225/300: dt: 0.9000, rms radial error=139.019, avgs=0 230/300: dt: 0.9000, rms radial error=138.237, avgs=0 235/300: dt: 0.9000, rms radial error=137.459, avgs=0 240/300: dt: 0.9000, rms radial error=136.686, avgs=0 245/300: dt: 0.9000, rms radial error=135.917, avgs=0 250/300: dt: 0.9000, rms radial error=135.152, avgs=0 255/300: dt: 0.9000, rms radial error=134.392, avgs=0 260/300: dt: 0.9000, rms radial error=133.635, avgs=0 265/300: dt: 0.9000, rms radial error=132.883, avgs=0 270/300: dt: 0.9000, rms radial error=132.135, avgs=0 275/300: dt: 0.9000, rms radial error=131.392, avgs=0 280/300: dt: 0.9000, rms radial error=130.652, avgs=0 285/300: dt: 0.9000, rms radial error=129.917, avgs=0 290/300: dt: 0.9000, rms radial error=129.185, avgs=0 295/300: dt: 0.9000, rms radial error=128.458, avgs=0 300/300: dt: 0.9000, rms radial error=127.735, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 6970.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 2 (K=80.0), pass 1, starting sse = 935.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00123 epoch 3 (K=320.0), pass 1, starting sse = 65.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/11 = 0.01402 epoch 4 (K=1280.0), pass 1, starting sse = 2.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00666 final diswriting spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours tance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Apr 20 18:14:10 EDT 2010 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 avg35rerun 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 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ before topology correction, eno=-8 (nv=136216, nf=272448, ne=408672, g=5) 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... 2354 ambiguous faces found in tessellation segmenting defects... 10 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 6 9 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2326 (-4.6163) -vertex loglikelihood: -5.9968 (-2.9984) -normal dot loglikelihood: -3.6391 (-3.6391) -quad curv loglikelihood: -6.2997 (-3.1498) Total Loglikelihood : -25.1682 CORRECTING DEFECT 0 (vertices=176, convex hull=76) After retessellation of defect 0, euler #=-7 (134926,404575,269642) : difference with theory (-6) = 1 CORRECTING DEFECT 1 (vertices=29, convex hull=56) After retessellation of defect 1, euler #=-6 (134935,404623,269682) : difference with theory (-5) = 1 CORRECTING DEFECT 2 (vertices=35, convex hull=34) After retessellation of defect 2, euler #=-5 (134937,404644,269702) : difference with theory (-4) = 1 CORRECTING DEFECT 3 (vertices=57, convex hull=41) After retessellation of defect 3, euler #=-4 (134944,404677,269729) : difference with theory (-3) = 1 CORRECTING DEFECT 4 (vertices=27, convex hull=63) After retessellation of defect 4, euler #=-3 (134953,404728,269772) : difference with theory (-2) = 1 CORRECTING DEFECT 5 (vertices=69, convex hull=51) After retessellation of defect 5, euler #=-2 (134964,404780,269814) : difference with theory (-1) = 1 CORRECTING DEFECT 6 (vertices=884, convex hull=166) After retessellation of defect 6, euler #=0 (134972,404889,269917) : difference with theory (0) = 0 CORRECTING DEFECT 7 (vertices=5, convex hull=13) After retessellation of defect 7, euler #=1 (134972,404892,269921) : difference with theory (1) = 0 CORRECTING DEFECT 8 (vertices=22, convex hull=48) After retessellation of defect 8, euler #=2 (134980,404934,269956) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.15-->6.29) (max @ vno 97602 --> 98653) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.15-->6.29) (max @ vno 97602 --> 98653) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 43 mutations (29.7%), 102 crossovers (70.3%), 138 vertices were eliminated building final representation... 1236 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134980, nf=269956, ne=404934, g=0) writing corrected surface to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.9 minutes 0 defective edges removing intersecting faces 000: 95 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 134980 - 404934 + 269956 = 2 --> 0 holes F =2V-4: 269956 = 269960-4 (0) 2E=3F: 809868 = 809868 (0) total defect index = 0 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make Final Surf rh Tue Apr 20 18:26:12 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs avg35rerun rh 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 1.113 2010/04/08 19:42:02 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/filled.mgz... reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... 12424 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.orig... computing class statistics... border white: 258602 voxels (1.54%) border gray 281737 voxels (1.68%) WM (99.0): 98.9 +- 7.4 [70.0 --> 110.0] GM (76.0) : 75.1 +- 9.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70) setting MAX_BORDER_WHITE to 109.4 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 50.5 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.05-->3.15) (max @ vno 97602 --> 98653) face area 0.29 +- 0.12 (0.00-->2.29) mean absolute distance = 0.75 +- 0.86 4990 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=69 using class modes intead of means.... mean inside = 94.8, mean outside = 78.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=80.5, 17 (17) missing vertices, mean dist 0.5 [0.5 (%31.4)->0.9 (%68.6))] %73 local maxima, %21 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 0.94 +- 0.26 (0.15-->5.72) (max @ vno 97602 --> 98653) face area 0.29 +- 0.13 (0.00-->3.38) mean absolute distance = 0.33 +- 0.63 1738 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4907576.5, rms=10.38 001: dt: 0.5000, sse=5065739.0, rms=7.78 002: dt: 0.5000, sse=5141631.0, rms=6.08 003: dt: 0.5000, sse=5338232.0, rms=4.86 004: dt: 0.5000, sse=5394298.5, rms=4.00 005: dt: 0.5000, sse=5518938.0, rms=3.44 006: dt: 0.5000, sse=5542902.5, rms=3.09 007: dt: 0.5000, sse=5630823.5, rms=2.90 008: dt: 0.5000, sse=5605243.0, rms=2.80 rms = 2.75, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5640434.0, rms=2.75 010: dt: 0.2500, sse=3106835.8, rms=1.65 011: dt: 0.2500, sse=2823997.0, rms=1.40 012: dt: 0.2500, sse=2727789.5, rms=1.34 rms = 1.31, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=2696757.5, rms=1.31 rms = 1.29, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=2663312.5, rms=1.29 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.7, 32 (10) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.3 (%29.9))] %77 local maxima, %18 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 0.94 +- 0.25 (0.13-->5.93) (max @ vno 97602 --> 98653) face area 0.37 +- 0.16 (0.00-->4.58) mean absolute distance = 0.28 +- 0.46 2685 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3161677.5, rms=3.86 015: dt: 0.5000, sse=3455872.2, rms=2.28 rms = 2.30, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=3210970.2, rms=1.78 017: dt: 0.2500, sse=3116405.2, rms=1.39 018: dt: 0.2500, sse=3049438.0, rms=1.23 019: dt: 0.2500, sse=3018946.5, rms=1.17 rms = 1.15, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3005430.8, rms=1.15 rms = 1.14, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=2982448.5, rms=1.14 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=85.1, 36 (8) missing vertices, mean dist -0.2 [0.3 (%73.5)->0.2 (%26.5))] %85 local maxima, %10 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 0.92 +- 0.24 (0.12-->6.07) (max @ vno 97602 --> 98653) face area 0.36 +- 0.16 (0.00-->4.76) mean absolute distance = 0.23 +- 0.33 3006 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3214311.8, rms=3.28 022: dt: 0.5000, sse=3534858.8, rms=2.19 rms = 2.36, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3334145.0, rms=1.60 024: dt: 0.2500, sse=3225130.5, rms=1.24 025: dt: 0.2500, sse=3178237.0, rms=1.11 rms = 1.08, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3158161.0, rms=1.08 rms = 1.06, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3137811.8, rms=1.06 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.1, 46 (6) missing vertices, mean dist -0.1 [0.2 (%60.9)->0.2 (%39.1))] %89 local maxima, % 5 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3170531.0, rms=1.76 028: dt: 0.5000, sse=3876481.5, rms=1.37 rms = 1.80, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3573966.5, rms=1.02 030: dt: 0.2500, sse=3430596.5, rms=0.93 rms = 0.89, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=3470715.0, rms=0.89 rms = 0.89, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3470715.0, rms=0.89 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group correcting aseg with surfaces... label Right_Hippocampus: removing 2 voxels in segment 1 label Right_Hippocampus: removing 4879 voxels in segment 2 label Right_Hippocampus: removing 1 voxels in segment 3 label Right_Hippocampus: removing 12 voxels in segment 4 generating cortex label... 11 non-cortical segments detected only using segment with 1940 vertices erasing segment 1 (vno[0] = 75494) erasing segment 2 (vno[0] = 79698) erasing segment 3 (vno[0] = 96471) erasing segment 4 (vno[0] = 97467) erasing segment 5 (vno[0] = 103641) erasing segment 6 (vno[0] = 103663) erasing segment 7 (vno[0] = 104432) erasing segment 8 (vno[0] = 106017) erasing segment 9 (vno[0] = 106746) erasing segment 10 (vno[0] = 106761) writing cortex label to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label/rh.cortex.label... LabelWrite: saving to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label/rh.cortex.label writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.area vertex spacing 0.92 +- 0.24 (0.06-->6.18) (max @ vno 97602 --> 98653) face area 0.36 +- 0.16 (0.00-->4.81) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=61.0, 45 (45) missing vertices, mean dist 1.8 [4.5 (%0.0)->2.4 (%100.0))] %15 local maxima, %58 large gradients and %23 min vals, 2009 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=19404618.0, rms=25.55 001: dt: 0.5000, sse=14915091.0, rms=21.94 002: dt: 0.5000, sse=11625308.0, rms=18.88 003: dt: 0.5000, sse=9288014.0, rms=16.32 004: dt: 0.5000, sse=7695235.0, rms=14.08 005: dt: 0.5000, sse=6552152.0, rms=12.14 006: dt: 0.5000, sse=5731527.0, rms=10.48 007: dt: 0.5000, sse=5129434.5, rms=9.03 008: dt: 0.5000, sse=4732994.5, rms=7.76 009: dt: 0.5000, sse=4439896.5, rms=6.63 010: dt: 0.5000, sse=4236491.5, rms=5.65 011: dt: 0.5000, sse=4079925.0, rms=4.79 012: dt: 0.5000, sse=3993303.2, rms=4.07 013: dt: 0.5000, sse=3924488.0, rms=3.51 014: dt: 0.5000, sse=3913654.0, rms=3.09 015: dt: 0.5000, sse=3912566.0, rms=2.78 016: dt: 0.5000, sse=3909717.2, rms=2.57 017: dt: 0.5000, sse=3905682.2, rms=2.41 018: dt: 0.5000, sse=3892484.5, rms=2.32 019: dt: 0.5000, sse=3895461.5, rms=2.24 rms = 2.20, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=3885327.8, rms=2.20 021: dt: 0.2500, sse=2891833.8, rms=1.76 022: dt: 0.2500, sse=2800120.2, rms=1.67 rms = 1.64, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2774979.0, rms=1.64 rms = 1.60, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=2720862.2, rms=1.60 positioning took 2.6 minutes mean border=59.7, 859 (14) missing vertices, mean dist 0.2 [0.2 (%55.9)->0.7 (%44.1))] %26 local maxima, %51 large gradients and %18 min vals, 467 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=3134318.8, rms=3.24 025: dt: 0.5000, sse=3367011.0, rms=2.42 026: dt: 0.5000, sse=3796479.8, rms=2.17 027: dt: 0.5000, sse=3885678.5, rms=2.08 rms = 2.09, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3394363.0, rms=1.76 029: dt: 0.2500, sse=3217311.5, rms=1.62 rms = 1.58, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3177191.5, rms=1.58 rms = 1.54, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3123354.0, rms=1.54 positioning took 0.8 minutes mean border=58.9, 1322 (13) missing vertices, mean dist 0.1 [0.2 (%52.7)->0.5 (%47.3))] %41 local maxima, %36 large gradients and %17 min vals, 425 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=3218862.5, rms=2.26 032: dt: 0.5000, sse=3427479.2, rms=1.85 rms = 1.84, time step reduction 1 of 3 to 0.250... 033: dt: 0.5000, sse=3782104.2, rms=1.84 034: dt: 0.2500, sse=3331516.2, rms=1.47 035: dt: 0.2500, sse=3282711.5, rms=1.41 rms = 1.39, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=3269132.8, rms=1.39 rms = 1.36, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=3220885.0, rms=1.36 positioning took 0.6 minutes mean border=58.1, 2619 (13) missing vertices, mean dist 0.1 [0.2 (%48.2)->0.4 (%51.8))] %53 local maxima, %24 large gradients and %16 min vals, 544 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3256817.2, rms=1.79 038: dt: 0.5000, sse=3402833.0, rms=1.57 rms = 1.60, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3275106.5, rms=1.38 040: dt: 0.2500, sse=3249025.0, rms=1.28 rms = 1.26, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=3233648.5, rms=1.26 rms = 1.24, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=3197759.0, rms=1.24 positioning took 0.6 minutes writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.area.pial vertex spacing 1.02 +- 0.41 (0.05-->7.62) (max @ vno 88622 --> 87491) face area 0.42 +- 0.30 (0.00-->4.70) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134980 vertices processed 25000 of 134980 vertices processed 50000 of 134980 vertices processed 75000 of 134980 vertices processed 100000 of 134980 vertices processed 125000 of 134980 vertices processed 0 of 134980 vertices processed 25000 of 134980 vertices processed 50000 of 134980 vertices processed 75000 of 134980 vertices processed 100000 of 134980 vertices processed 125000 of 134980 vertices processed thickness calculation complete, 2074:2029 truncations. 66645 vertices at 0 distance 82851 vertices at 1 distance 64733 vertices at 2 distance 26528 vertices at 3 distance 10302 vertices at 4 distance 3882 vertices at 5 distance 1586 vertices at 6 distance 734 vertices at 7 distance 348 vertices at 8 distance 204 vertices at 9 distance 124 vertices at 10 distance 85 vertices at 11 distance 55 vertices at 12 distance 58 vertices at 13 distance 38 vertices at 14 distance 33 vertices at 15 distance 20 vertices at 16 distance 28 vertices at 17 distance 26 vertices at 18 distance 27 vertices at 19 distance 51 vertices at 20 distance writing curvature file /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.thickness positioning took 14.2 minutes #-------------------------------------------- #@# Surf Volume rh Tue Apr 20 18:40:24 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf mris_calc -o rh.area.mid rh.area add rh.area.pial mris_calc -o rh.area.mid rh.area.mid div 2 mris_calc -o rh.volume rh.area.mid mul rh.thickness #-------------------------------------------- #@# Smooth2 rh Tue Apr 20 18:40:25 EDT 2010 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 Apr 20 18:40:30 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.7 mm, total surface area = 87207 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.111 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.018 (target=0.015) step 045: 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/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 ~ [-0.21 0.25], k2 ~ [-0.09 0.05] total integrated curvature = 0.592*4pi (7.437) --> 0 handles ICI = 1.7, FI = 12.3, variation=203.505 148 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 = 0.001 145 vertices thresholded to be in [-0.13 0.13] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Tue Apr 20 18:42:51 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm avg35rerun 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 [ avg35rerun/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 268 ] WARN: S lookup min: -0.164050 WARN: S explicit min: 0.000000 vertex = 110 #-------------------------------------------- #@# Sphere rh Tue Apr 20 18:42:57 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 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 1.14 hours scaling brain by 0.276... pass 1: epoch 1 of 3 starting distance error %20.07 pass 1: epoch 2 of 3 starting distance error %20.03 unfolding complete - removing small folds... starting distance error %19.97 removing remaining folds... final distance error %19.97 153: 0 negative triangles #-------------------------------------------- #@# Surf Reg rh Tue Apr 20 19:51:35 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.605 curvature mean = 0.027, std = 0.921 curvature mean = 0.015, std = 0.850 curvature mean = 0.016, std = 0.943 curvature mean = 0.007, std = 0.940 curvature mean = 0.013, std = 0.951 curvature mean = 0.003, std = 0.974 curvature mean = 0.013, std = 0.951 curvature mean = 0.000, std = 0.990 curvature mean = -0.020, std = 0.249 curvature mean = 0.006, std = 0.070 curvature mean = 0.046, std = 0.407 curvature mean = 0.007, std = 0.084 curvature mean = 0.017, std = 0.622 curvature mean = 0.007, std = 0.090 curvature mean = 0.009, std = 0.759 curvature mean = 0.007, std = 0.093 curvature mean = 0.002, std = 0.852 expanding nbhd size to 1 196: 0 negative triangles #-------------------------------------------- #@# Jacobian white rh Tue Apr 20 20:48:41 EDT 2010 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 Apr 20 20:48:43 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev/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/dev/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Apr 20 20:48:46 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 avg35rerun rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/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 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 1064 labels changed using aseg relabeling using gibbs priors... 000: 2987 changed, 134980 examined... 001: 670 changed, 12697 examined... 002: 168 changed, 3804 examined... 003: 41 changed, 1012 examined... 004: 23 changed, 245 examined... 005: 7 changed, 140 examined... 006: 2 changed, 50 examined... 007: 1 changed, 13 examined... 008: 1 changed, 5 examined... 009: 1 changed, 9 examined... 010: 2 changed, 9 examined... 011: 0 changed, 11 examined... 201 labels changed using aseg 000: 104 total segments, 63 labels (310 vertices) changed 001: 43 total segments, 2 labels (9 vertices) changed 002: 40 total segments, 1 labels (7 vertices) changed 003: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1057 vertices marked for relabeling... 1057 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 53 seconds. #----------------------------------------- #@# Parcellation Stats rh Tue Apr 20 20:49:39 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 avg35rerun rh computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert and SurfArea. 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 1272 899 1831 1.977 0.553 0.108 0.022 10 1.1 bankssts 1087 736 1725 2.438 0.729 0.143 0.036 16 1.3 caudalanteriorcingulate 2509 1761 4726 2.360 0.630 0.129 0.032 25 3.2 caudalmiddlefrontal 2527 1860 4230 2.279 0.691 0.156 0.046 30 4.8 cuneus 472 340 1711 3.523 1.068 0.134 0.029 4 0.6 entorhinal 5277 3805 10574 2.649 0.732 0.138 0.043 71 10.1 fusiform 8768 6307 16700 2.325 0.744 0.133 0.037 94 12.6 inferiorparietal 4993 3574 10947 2.655 0.918 0.134 0.037 54 7.2 inferiortemporal 1358 909 2811 2.904 1.027 0.133 0.042 16 2.1 isthmuscingulate 7545 5411 13688 2.491 0.646 0.147 0.041 79 12.6 lateraloccipital 3788 2747 8310 2.818 0.898 0.151 0.043 52 6.7 lateralorbitofrontal 4631 3362 7456 2.182 0.581 0.153 0.050 98 10.4 lingual 2829 2087 6281 2.574 0.833 0.140 0.037 57 4.4 medialorbitofrontal 5267 3739 12853 2.819 0.909 0.139 0.035 62 7.8 middletemporal 1119 755 2044 2.587 0.846 0.111 0.025 8 1.1 parahippocampal 2215 1508 2951 1.872 0.469 0.113 0.023 15 2.2 paracentral 1835 1243 3542 2.317 0.760 0.120 0.031 16 2.4 parsopercularis 1229 860 2919 2.650 0.862 0.141 0.037 17 1.8 parsorbitalis 2186 1558 4253 2.230 0.770 0.149 0.049 29 4.1 parstriangularis 2123 1489 2198 1.693 0.462 0.137 0.044 26 4.0 pericalcarine 6413 4285 8979 1.847 0.728 0.116 0.027 48 6.9 postcentral 1574 1103 2924 2.513 0.854 0.155 0.049 27 2.7 posteriorcingulate 8192 5427 12343 2.078 0.632 0.116 0.028 63 9.2 precentral 5195 3646 8838 2.253 0.743 0.131 0.034 56 7.1 precuneus 827 603 1699 2.410 0.719 0.147 0.044 13 1.5 rostralanteriorcingulate 8080 5738 15377 2.234 0.776 0.157 0.054 129 16.3 rostralmiddlefrontal 10301 7282 21052 2.435 0.744 0.133 0.039 112 15.3 superiorfrontal 8429 5911 13448 2.065 0.556 0.130 0.032 78 10.8 superiorparietal 5167 3542 10952 2.632 0.859 0.119 0.029 49 5.8 superiortemporal 4893 3484 10200 2.463 0.824 0.124 0.032 43 6.1 supramarginal 346 282 1168 3.051 0.556 0.246 0.110 10 1.6 frontalpole 564 390 2386 4.043 0.758 0.133 0.044 6 1.0 temporalpole 549 347 952 2.522 0.510 0.133 0.036 5 0.7 transversetemporal 3029 2146 6775 3.097 1.197 0.110 0.036 27 3.7 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Apr 20 20:49:54 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 avg35rerun rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/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 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.672 2010/04/14 14:42:36 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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: 9511 changed, 134980 examined... 001: 2241 changed, 36488 examined... 002: 702 changed, 11642 examined... 003: 306 changed, 3921 examined... 004: 151 changed, 1672 examined... 005: 76 changed, 866 examined... 006: 52 changed, 437 examined... 007: 28 changed, 287 examined... 008: 17 changed, 157 examined... 009: 9 changed, 107 examined... 010: 6 changed, 48 examined... 011: 4 changed, 39 examined... 012: 1 changed, 18 examined... 013: 2 changed, 7 examined... 014: 3 changed, 10 examined... 015: 2 changed, 13 examined... 016: 1 changed, 11 examined... 017: 0 changed, 5 examined... 24 labels changed using aseg 000: 295 total segments, 215 labels (2757 vertices) changed 001: 109 total segments, 30 labels (97 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 544 vertices marked for relabeling... 544 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Apr 20 20:50:55 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 avg35rerun rh computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert and SurfArea. 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 918 670 2095 2.490 0.853 0.180 0.080 22 2.1 G_and_S_frontomargin 1278 916 2945 2.927 0.676 0.155 0.045 15 2.3 G_and_S_occipital_inf 1200 818 1530 1.648 0.346 0.121 0.029 9 1.4 G_and_S_paracentral 1740 1204 3409 2.408 0.754 0.133 0.032 18 2.2 G_and_S_subcentral 854 652 2447 2.819 0.838 0.204 0.086 18 3.0 G_and_S_transv_frontopol 2793 1982 4924 2.206 0.683 0.134 0.039 34 4.2 G_and_S_cingul-Ant 1477 1018 2290 2.045 0.635 0.129 0.032 16 1.7 G_and_S_cingul-Mid-Ant 1352 946 2187 2.143 0.601 0.120 0.028 13 1.5 G_and_S_cingul-Mid-Post 557 379 1711 3.755 0.655 0.190 0.083 11 1.8 G_cingul-Post-dorsal 260 176 796 3.418 0.749 0.139 0.041 3 0.3 G_cingul-Post-ventral 2387 1784 3846 2.146 0.750 0.162 0.049 30 4.7 G_cuneus 1370 927 3341 2.697 0.586 0.137 0.043 19 2.3 G_front_inf-Opercular 322 239 682 2.345 0.545 0.167 0.068 7 0.6 G_front_inf-Orbital 1199 853 3115 2.672 0.717 0.178 0.062 22 3.0 G_front_inf-Triangul 3891 2807 9904 2.652 0.691 0.173 0.057 77 8.9 G_front_middle 7143 5043 16524 2.626 0.700 0.143 0.043 89 12.0 G_front_sup 403 314 1389 3.916 1.142 0.121 0.042 5 0.6 G_Ins_lg_and_S_cent_ins 553 399 1778 3.594 1.054 0.140 0.047 10 1.1 G_insular_short 2761 1996 6673 2.744 0.689 0.155 0.049 38 5.4 G_occipital_middle 1874 1406 4052 2.378 0.665 0.152 0.039 22 3.0 G_occipital_sup 2182 1570 4870 2.692 0.680 0.154 0.043 36 3.8 G_oc-temp_lat-fusifor 3037 2214 5264 2.169 0.568 0.152 0.044 37 5.5 G_oc-temp_med-Lingual 1524 1067 4083 3.091 1.049 0.133 0.064 24 4.5 G_oc-temp_med-Parahip 2685 1954 7715 3.040 0.840 0.160 0.047 45 5.1 G_orbital 3106 2320 7724 2.609 0.718 0.156 0.042 45 5.2 G_pariet_inf-Angular 2405 1744 6794 2.876 0.886 0.142 0.040 29 3.6 G_pariet_inf-Supramar 2449 1744 4488 2.177 0.490 0.135 0.035 24 3.5 G_parietal_sup 2392 1578 3756 1.985 0.647 0.126 0.030 20 3.0 G_postcentral 2797 1802 5280 2.346 0.628 0.114 0.027 21 3.1 G_precentral 2429 1744 5237 2.454 0.605 0.152 0.040 36 3.9 G_precuneus 825 656 2393 2.691 0.752 0.167 0.047 14 1.6 G_rectus 156 124 406 3.084 0.924 0.093 0.070 22 0.3 G_subcallosal 382 238 755 2.583 0.450 0.129 0.032 4 0.5 G_temp_sup-G_T_transv 1640 1100 4606 3.032 0.731 0.143 0.044 24 2.6 G_temp_sup-Lateral 677 482 1662 3.094 0.812 0.087 0.017 3 0.4 G_temp_sup-Plan_polar 795 577 1682 2.559 0.686 0.113 0.022 6 0.8 G_temp_sup-Plan_tempo 2500 1854 6949 2.981 0.815 0.146 0.042 35 4.0 G_temporal_inf 3232 2326 9626 3.145 0.797 0.156 0.044 48 5.8 G_temporal_middle 377 272 456 1.703 0.493 0.106 0.017 2 0.3 Lat_Fis-ant-Horizont 204 133 343 2.362 0.490 0.103 0.022 1 0.2 Lat_Fis-ant-Vertical 1434 985 1891 2.145 0.649 0.107 0.025 8 1.4 Lat_Fis-post 3204 2319 5111 2.078 0.640 0.148 0.043 34 5.5 Pole_occipital 1736 1235 6398 3.579 1.068 0.153 0.048 24 3.4 Pole_temporal 2117 1444 2499 2.007 0.707 0.133 0.062 66 6.4 S_calcarine 2992 1970 2656 1.459 0.529 0.103 0.022 16 2.8 S_central 1333 905 1591 1.848 0.479 0.110 0.029 10 1.3 S_cingul-Marginalis 663 463 1201 2.977 0.850 0.128 0.030 5 0.8 S_circular_insula_ant 1395 909 1913 2.341 1.069 0.070 0.011 4 0.7 S_circular_insula_inf 1352 924 1536 1.815 0.527 0.098 0.021 6 1.3 S_circular_insula_sup 894 613 1111 1.951 0.501 0.094 0.017 4 0.6 S_collat_transv_ant 725 527 887 2.224 0.379 0.149 0.043 7 1.1 S_collat_transv_post 1916 1339 2287 1.709 0.478 0.118 0.029 14 2.1 S_front_inf 1713 1200 2512 2.003 0.581 0.142 0.046 19 2.9 S_front_middle 2366 1667 3008 1.900 0.507 0.107 0.022 14 2.2 S_front_sup 322 219 328 1.947 0.531 0.113 0.024 2 0.4 S_interm_prim-Jensen 3846 2601 4662 1.867 0.446 0.122 0.028 32 4.5 S_intrapariet_and_P_trans 1571 1102 2429 2.526 0.557 0.130 0.032 12 2.2 S_oc_middle_and_Lunatus 1456 1017 1968 2.322 0.424 0.119 0.027 10 1.6 S_oc_sup_and_transversal 875 649 1684 2.739 0.402 0.126 0.037 8 1.5 S_occipital_ant 1372 933 1649 2.186 0.631 0.109 0.026 8 1.5 S_oc-temp_lat 2136 1543 3248 2.526 0.642 0.125 0.025 18 2.3 S_oc-temp_med_and_Lingual 562 392 673 1.858 0.544 0.136 0.036 5 0.9 S_orbital_lateral 887 658 1557 2.604 0.639 0.109 0.020 6 0.7 S_orbital_med-olfact 1332 938 2208 2.447 1.002 0.134 0.037 13 2.2 S_orbital-H_Shaped 1902 1281 2327 2.012 0.659 0.115 0.026 14 2.0 S_parieto_occipital 1441 918 1849 2.573 0.794 0.125 0.027 19 1.4 S_pericallosal 2481 1658 2734 1.776 0.446 0.095 0.020 12 1.9 S_postcentral 1414 965 1868 2.024 0.454 0.122 0.027 12 1.5 S_precentral-inf-part 1807 1263 2244 1.958 0.394 0.118 0.032 13 2.2 S_precentral-sup-part 404 292 913 3.109 1.198 0.150 0.032 5 0.5 S_suborbital 1138 793 1740 2.301 0.866 0.143 0.043 13 1.9 S_subparietal 1471 1035 2046 2.331 0.778 0.122 0.028 10 1.8 S_temporal_inf 5870 4099 7751 1.967 0.611 0.109 0.024 42 5.4 S_temporal_sup 336 251 639 2.918 0.586 0.160 0.037 4 0.5 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Tue Apr 20 20:51:12 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance avg35rerun SUBJECTS_DIR is /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun 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 = 35 writing volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Apr 20 21:05:30 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun 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/dev/ASegStatsLUT.txt --subject avg35rerun atlas_icv (eTIV) = 1155311 mm^3 (det: 1.686217 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 270024 rh white matter volume 262190 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 291603.621163, pTot = 520211.728107 c = 228608.106944 rh surface-based volumes (mm3): wTot = 283055.440096, pTot = 519109.862002 c = 236054.421906 Computing SupraTentVolCor SupraTentVolCor = 72891.000 SupraTentVol = 1112212.590 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 5441 5441 4 5 Left-Inf-Lat-Vent 33 33 5 7 Left-Cerebellum-White-Matter 24970 24970 6 8 Left-Cerebellum-Cortex 53801 53801 7 10 Left-Thalamus-Proper 7843 7843 8 11 Left-Caudate 4431 4431 9 12 Left-Putamen 7285 7285 10 13 Left-Pallidum 1768 1768 11 14 3rd-Ventricle 1324 1324 12 15 4th-Ventricle 2370 2370 13 16 Brain-Stem 21800 21800 14 17 Left-Hippocampus 4580 4580 15 18 Left-Amygdala 1622 1622 16 24 CSF 1340 1340 17 26 Left-Accumbens-area 689 689 18 28 Left-VentralDC 4808 4808 19 30 Left-vessel 85 85 20 31 Left-choroid-plexus 1469 1469 23 43 Right-Lateral-Ventricle 5442 5442 24 44 Right-Inf-Lat-Vent 157 157 25 46 Right-Cerebellum-White-Matter 22953 22953 26 47 Right-Cerebellum-Cortex 59107 59107 27 49 Right-Thalamus-Proper 7582 7582 28 50 Right-Caudate 4380 4380 29 51 Right-Putamen 7154 7154 30 52 Right-Pallidum 1776 1776 31 53 Right-Hippocampus 4402 4402 32 54 Right-Amygdala 1669 1669 33 58 Right-Accumbens-area 981 981 34 60 Right-VentralDC 4477 4477 35 62 Right-vessel 30 30 36 63 Right-choroid-plexus 1475 1475 37 72 5th-Ventricle 0 38 77 WM-hypointensities 3188 3188 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 17 17 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 364 364 45 251 CC_Posterior 1037 1037 46 252 CC_Mid_Posterior 468 468 47 253 CC_Central 449 449 48 254 CC_Mid_Anterior 422 422 49 255 CC_Anterior 907 907 Reporting on 45 segmentations SubCortGrayVol = 200155 #----------------------------------------- #@# AParc-to-ASeg Tue Apr 20 21:15:27 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun mri_aparc2aseg --s avg35rerun --volmask SUBJECTS_DIR /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun subject avg35rerun outvol /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading lh pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial Loading lh annotations from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading rh pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial Loading rh annotations from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 457429 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aparc+aseg.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun mri_aparc2aseg --s avg35rerun --volmask --a2009s SUBJECTS_DIR /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun subject avg35rerun outvol /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading lh pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial Loading lh annotations from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading rh pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial Loading rh annotations from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 457429 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Apr 20 21:18:04 EDT 2010 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun mri_aparc2aseg --s avg35rerun --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun subject avg35rerun outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading lh pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial Loading lh annotations from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading rh pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial Loading rh annotations from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/ribbon.mgz Loading filled from /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8108 vertices from left hemi Ripped 8391 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 958824 Used brute-force search on 767 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1.000000 1 k 1.000000 2 k 1882.000000 3 k 3.000000 4 k 2.000000 5 k 4.000000 Fixing Parahip RH WM Found 6 clusters 0 k 1.000000 1 k 2009.000000 2 k 1.000000 3 k 1.000000 4 k 5.000000 5 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun 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 avg35rerun --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv atlas_icv (eTIV) = 1155311 mm^3 (det: 1.686217 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 270024 rh white matter volume 262190 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1610615 # brainmaskvolume 1610615.0 # nbrainsegvoxels 268436 # brainsegvolume 268436.0 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 3435 3435 2 3002 wm-lh-caudalanteriorcingulate 2936 2936 3 3003 wm-lh-caudalmiddlefrontal 7850 7850 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2532 2532 6 3006 wm-lh-entorhinal 1076 1076 7 3007 wm-lh-fusiform 8636 8636 8 3008 wm-lh-inferiorparietal 9750 9750 9 3009 wm-lh-inferiortemporal 8914 8914 10 3010 wm-lh-isthmuscingulate 3688 3688 11 3011 wm-lh-lateraloccipital 11898 11898 12 3012 wm-lh-lateralorbitofrontal 6724 6724 13 3013 wm-lh-lingual 7271 7271 14 3014 wm-lh-medialorbitofrontal 3546 3546 15 3015 wm-lh-middletemporal 6501 6501 16 3016 wm-lh-parahippocampal 2031 2031 17 3017 wm-lh-paracentral 3413 3413 18 3018 wm-lh-parsopercularis 3109 3109 19 3019 wm-lh-parsorbitalis 1150 1150 20 3020 wm-lh-parstriangularis 3205 3205 21 3021 wm-lh-pericalcarine 3321 3321 22 3022 wm-lh-postcentral 10251 10251 23 3023 wm-lh-posteriorcingulate 4379 4379 24 3024 wm-lh-precentral 15991 15991 25 3025 wm-lh-precuneus 8925 8925 26 3026 wm-lh-rostralanteriorcingulate 3086 3086 27 3027 wm-lh-rostralmiddlefrontal 11253 11253 28 3028 wm-lh-superiorfrontal 18721 18721 29 3029 wm-lh-superiorparietal 13432 13432 30 3030 wm-lh-superiortemporal 7287 7287 31 3031 wm-lh-supramarginal 8396 8396 32 3032 wm-lh-frontalpole 301 301 33 3033 wm-lh-temporalpole 768 768 34 3034 wm-lh-transversetemporal 836 836 35 3035 wm-lh-insula 9724 9724 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 2691 2691 120 4002 wm-rh-caudalanteriorcingulate 3092 3092 121 4003 wm-rh-caudalmiddlefrontal 4600 4600 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 3318 3318 124 4006 wm-rh-entorhinal 764 764 125 4007 wm-rh-fusiform 7761 7761 126 4008 wm-rh-inferiorparietal 12676 12676 127 4009 wm-rh-inferiortemporal 7388 7388 128 4010 wm-rh-isthmuscingulate 3391 3391 129 4011 wm-rh-lateraloccipital 11795 11795 130 4012 wm-rh-lateralorbitofrontal 6995 6995 131 4013 wm-rh-lingual 6968 6968 132 4014 wm-rh-medialorbitofrontal 4114 4114 133 4015 wm-rh-middletemporal 6957 6957 134 4016 wm-rh-parahippocampal 2177 2177 135 4017 wm-rh-paracentral 4442 4442 136 4018 wm-rh-parsopercularis 2813 2813 137 4019 wm-rh-parsorbitalis 1217 1217 138 4020 wm-rh-parstriangularis 3204 3204 139 4021 wm-rh-pericalcarine 3451 3451 140 4022 wm-rh-postcentral 8773 8773 141 4023 wm-rh-posteriorcingulate 4239 4239 142 4024 wm-rh-precentral 15362 15362 143 4025 wm-rh-precuneus 8334 8334 144 4026 wm-rh-rostralanteriorcingulate 2168 2168 145 4027 wm-rh-rostralmiddlefrontal 12677 12677 146 4028 wm-rh-superiorfrontal 17652 17652 147 4029 wm-rh-superiorparietal 12699 12699 148 4030 wm-rh-superiortemporal 6232 6232 149 4031 wm-rh-supramarginal 8710 8710 150 4032 wm-rh-frontalpole 408 408 151 4033 wm-rh-temporalpole 585 585 152 4034 wm-rh-transversetemporal 600 600 153 4035 wm-rh-insula 8470 8470 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 37212 37212 237 5002 Right-UnsegmentedWhiteMatter 36433 36433 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 SubCortGrayVol = 0 /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label #-------------------------------------------- #@# BA Labels lh Tue Apr 20 21:36:58 EDT 2010 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... ln -s /usr/local/freesurfer/dev/subjects/fsaverage /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA1.label --trgsubject avg35rerun --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 681 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA2.label --trgsubject avg35rerun --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 1349 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA3a.label --trgsubject avg35rerun --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 162 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA3b.label --trgsubject avg35rerun --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 416 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA4a.label --trgsubject avg35rerun --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 378 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA4p.label --trgsubject avg35rerun --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 321 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA6.label --trgsubject avg35rerun --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 1459 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA44.label --trgsubject avg35rerun --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 401 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA45.label --trgsubject avg35rerun --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 763 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.V1.label --trgsubject avg35rerun --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 1158 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.V2.label --trgsubject avg35rerun --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 3111 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.MT.label --trgsubject avg35rerun --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 661 Checking for and removing duplicates Writing label file ./lh.MT.label LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s avg35rerun --hemi lh --ctab /usr/local/freesurfer/dev/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 /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.16 2010/02/22 23:00:01 nicks Exp $ cwd /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label cmdline mris_label2annot --s avg35rerun --hemi lh --ctab /usr/local/freesurfer/dev/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-0-38.local machine x86_64 user lzollei subject avg35rerun hemi lh SUBJECTS_DIR /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 96487 unhit vertices Writing annot to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab avg35rerun lh computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /usr/local/freesurfer/dev/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 1285 815 1699 1.770 0.451 0.120 0.029 10 1.5 BA1 5189 3563 6755 1.851 0.584 0.115 0.026 37 5.5 BA2 1067 700 782 1.390 0.405 0.128 0.034 9 1.4 BA3a 2427 1624 2977 1.631 0.638 0.121 0.028 20 2.8 BA3b 1674 1063 2302 1.975 0.551 0.106 0.023 10 1.7 BA4a 1527 935 1856 1.997 0.633 0.091 0.018 8 1.2 BA4p 9733 6547 17791 2.354 0.717 0.120 0.030 81 11.8 BA6 2487 1758 4584 2.204 0.611 0.139 0.034 33 3.5 BA44 3133 2230 5461 2.028 0.741 0.143 0.042 38 5.1 BA45 3250 2390 4947 2.061 0.743 0.150 0.060 61 7.9 V1 8674 6134 13726 2.189 0.605 0.153 0.043 108 15.4 V2 2403 1659 4066 2.467 0.544 0.139 0.040 26 3.8 MT #-------------------------------------------- #@# BA Labels rh Tue Apr 20 21:39:09 EDT 2010 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA1.label --trgsubject avg35rerun --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 274 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA2.label --trgsubject avg35rerun --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 371 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA3a.label --trgsubject avg35rerun --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA3b.label --trgsubject avg35rerun --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 288 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA4a.label --trgsubject avg35rerun --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 297 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA4p.label --trgsubject avg35rerun --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 137 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA6.label --trgsubject avg35rerun --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 1216 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA44.label --trgsubject avg35rerun --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 818 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA45.label --trgsubject avg35rerun --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 1074 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.V1.label --trgsubject avg35rerun --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 1320 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.V2.label --trgsubject avg35rerun --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 3215 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.MT.label --trgsubject avg35rerun --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = avg35rerun 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/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white Reading target registration /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 = 672 Checking for and removing duplicates Writing label file ./rh.MT.label LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s avg35rerun --hemi rh --ctab /usr/local/freesurfer/dev/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 /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.16 2010/02/22 23:00:01 nicks Exp $ cwd /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label cmdline mris_label2annot --s avg35rerun --hemi rh --ctab /usr/local/freesurfer/dev/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-0-38.local machine x86_64 user lzollei subject avg35rerun hemi rh SUBJECTS_DIR /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 93254 unhit vertices Writing annot to /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab avg35rerun rh computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /usr/local/freesurfer/dev/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 929 593 1592 2.154 0.652 0.134 0.034 9 1.2 BA1 3298 2207 4333 1.899 0.572 0.104 0.022 20 3.0 BA2 1061 665 806 1.415 0.482 0.129 0.031 9 1.5 BA3a 2090 1411 2426 1.493 0.616 0.114 0.026 15 2.2 BA3b 1373 927 2049 1.939 0.532 0.094 0.018 6 1.1 BA4a 1193 796 1394 1.760 0.566 0.097 0.021 6 1.0 BA4p 8811 5978 16317 2.407 0.648 0.120 0.030 72 10.5 BA6 3607 2469 6239 2.216 0.680 0.121 0.031 32 4.3 BA44 4467 3141 9170 2.355 0.834 0.147 0.044 60 7.7 BA45 3781 2724 5204 1.827 0.627 0.135 0.041 40 6.5 V1 8723 6306 14552 2.290 0.605 0.155 0.049 145 18.3 V2 2393 1736 4760 2.749 0.519 0.138 0.040 23 4.0 MT /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Tue Apr 20 21:41:17 EDT 2010 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... ln -s /usr/local/freesurfer/dev/subjects/lh.EC_average /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/lh.EC_average mris_spherical_average -erode 1 -orig white -t 0.4 -o avg35rerun label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject avg35rerun. processing subject lh.EC_average... reading output surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 1005 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 avg35rerun lh limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/lh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 350 212 1127 3.136 1.087 0.110 0.026 3 0.4 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Tue Apr 20 21:41:35 EDT 2010 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... ln -s /usr/local/freesurfer/dev/subjects/rh.EC_average /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/rh.EC_average mris_spherical_average -erode 1 -orig white -t 0.4 -o avg35rerun label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject avg35rerun. processing subject rh.EC_average... reading output surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 733 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 avg35rerun rh limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/wm.mgz... reading input surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.white... reading input pial surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/surf/rh.pial... reading input white surface /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/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 243 175 871 3.075 0.952 0.126 0.025 2 0.3 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s avg35rerun finished without error at Tue Apr 20 21:41:54 EDT 2010