Wed Jan 27 12:11:54 EST 2016 /space/freesurfer/subjects/test/bert.Darwin /usr/local/freesurfer/dev/bin/recon-all -s bert.Darwin -all subjid bert.Darwin setenv SUBJECTS_DIR /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Actual FREESURFER_HOME /usr/local/freesurfer/dev build-stamp.txt: freesurfer-Darwin-OSX-dev-20160126 Darwin gust.nmr.mgh.harvard.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 i386 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited descriptors 2560 memorylocked unlimited maxproc 709 PhysMem: 1558M wired, 3183M active, 161M inactive, 4902M used, 2871M free. ######################################## program versions used $Id: FreeSurferEnv.csh,v 1.87 2015/06/30 19:04:20 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:11:57-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:11:59-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:00-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:01-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:02-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:03-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:03-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:05-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:05-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:06-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_ca_normalize.c,v 1.65 2015/10/10 17:28:19 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:07-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_ca_register.c,v 1.94 2015/11/24 20:36:25 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:08-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:09-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:09-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:10-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:11-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:11-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:12-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:13-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:14-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:14-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:15-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_fix_topology.c,v 1.49 2015/11/24 20:36:25 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:16-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:17-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:17-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:18-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:19-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:20-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:21-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:21-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:22-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:23-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:24-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:25-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:25-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:26-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:27-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:27-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/27-17:12:28-GMT BuildTimeStamp: Jan 26 2016 12:51:57 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: zkaufman Machine: gust.nmr.mgh.harvard.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/dev/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/dev/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Jan 27 12:12:29 EST 2016 Found 3 runs /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /space/freesurfer/subjects/test/bert.Darwin \n mri_robust_template --mov /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.mgz --average 1 --template /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001-iscale.txt /space/freesurfer/subjects/test/bert.Darwin/mri/orig/002-iscale.txt /space/freesurfer/subjects/test/bert.Darwin/mri/orig/003-iscale.txt --subsample 200 --lta /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.lta /space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.lta /space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.lta \n $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ --mov: Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz as movable/source volume. --mov: Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.mgz as movable/source volume. --mov: Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz'... converting source '/space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.mgz'... converting source '/space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.mgz'... converting source '/space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /space/freesurfer/subjects/test/bert.Darwin/mri/orig/002.mgz ) to TP 1 ( /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /space/freesurfer/subjects/test/bert.Darwin/mri/orig/003.mgz ) to TP 1 ( /space/freesurfer/subjects/test/bert.Darwin/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: mapping movs and creating initial template... allow intensity scaling using median Writing final template: /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 3 minutes and 18 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /space/freesurfer/subjects/test/bert.Darwin \n mri_convert /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz --conform \n mri_convert /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /space/freesurfer/subjects/test/bert.Darwin/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) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz... \n mri_add_xform_to_header -c /space/freesurfer/subjects/test/bert.Darwin/mri/transforms/talairach.xfm /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jan 27 12:16:08 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /space/freesurfer/subjects/test/bert.Darwin/mri /usr/local/freesurfer/dev/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: FreeSurferEnv.csh,v 1.87 2015/06/30 19:04:20 nicks Exp $ Darwin gust.nmr.mgh.harvard.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 i386 Wed Jan 27 12:16:11 EST 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 tmpdir is ./tmp.mri_nu_correct.mni.72248 /space/freesurfer/subjects/test/bert.Darwin/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.72248/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.72248/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl 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.72248/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Wed Jan 27 12:16:34 EST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.72248/nu0.mnc ./tmp.mri_nu_correct.mni.72248/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.72248/0/ -iterations 1000 -distance 50 [zkaufman@gust.nmr.mgh.harvard.edu:/autofs/cluster/freesurfer/subjects/test/bert.Darwin/mri/] [2016-01-27 12:16:35] running: /usr/local/freesurfer/dev/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.72248/0/ ./tmp.mri_nu_correct.mni.72248/nu0.mnc ./tmp.mri_nu_correct.mni.72248/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 26 CV of field change: 0.000987714 Outputting Volume: ............................................................ Reading Volume: ............................................................... Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.72248/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.72248/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.72248/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Wed Jan 27 12:22:37 EST 2016 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi log file is transforms/talairach_avi.log... Started at Wed Jan 27 12:22:39 EST 2016 Ended at Wed Jan 27 12:24:04 EST 2016 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Wed Jan 27 12:24:07 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7584, pval=0.6675 >= threshold=0.0050) \n awk -f /usr/local/freesurfer/dev/bin/extract_talairach_avi_QA.awk /space/freesurfer/subjects/test/bert.Darwin/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /space/freesurfer/subjects/test/bert.Darwin/mri/transforms/talairach_avi.log \n TalAviQA: 0.97388 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Jan 27 12:24:08 EST 2016 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 \n /space/freesurfer/subjects/test/bert.Darwin/mri /usr/local/freesurfer/dev/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: FreeSurferEnv.csh,v 1.87 2015/06/30 19:04:20 nicks Exp $ Darwin gust.nmr.mgh.harvard.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 i386 Wed Jan 27 12:24:10 EST 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 tmpdir is ./tmp.mri_nu_correct.mni.72906 /space/freesurfer/subjects/test/bert.Darwin/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.72906/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.72906/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl 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.72906/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Wed Jan 27 12:24:32 EST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.72906/nu0.mnc ./tmp.mri_nu_correct.mni.72906/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.72906/0/ [zkaufman@gust.nmr.mgh.harvard.edu:/autofs/cluster/freesurfer/subjects/test/bert.Darwin/mri/] [2016-01-27 12:24:33] 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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.72906/0/ ./tmp.mri_nu_correct.mni.72906/nu0.mnc ./tmp.mri_nu_correct.mni.72906/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000964954 Outputting Volume: ............................................................ Reading Volume: ............................................................... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Wed Jan 27 12:29:49 EST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.72906/nu1.mnc ./tmp.mri_nu_correct.mni.72906/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.72906/1/ [zkaufman@gust.nmr.mgh.harvard.edu:/autofs/cluster/freesurfer/subjects/test/bert.Darwin/mri/] [2016-01-27 12:29:50] 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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.72906/1/ ./tmp.mri_nu_correct.mni.72906/nu1.mnc ./tmp.mri_nu_correct.mni.72906/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 9 CV of field change: 0.000963165 Outputting Volume: ............................................................ Reading Volume: ............................................................... Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.72906/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.72906/ones.mgz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.72906/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.72906/ones.mgz sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman input ./tmp.mri_nu_correct.mni.72906/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.72906/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.72906/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.72906/sum.junk --avgwf ./tmp.mri_nu_correct.mni.72906/input.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.72906/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.72906/sum.junk --avgwf ./tmp.mri_nu_correct.mni.72906/input.mean.dat sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.72906/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.72906/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.72906/ones.mgz --i ./tmp.mri_nu_correct.mni.72906/nu2.mnc --sum ./tmp.mri_nu_correct.mni.72906/sum.junk --avgwf ./tmp.mri_nu_correct.mni.72906/output.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.72906/ones.mgz --i ./tmp.mri_nu_correct.mni.72906/nu2.mnc --sum ./tmp.mri_nu_correct.mni.72906/sum.junk --avgwf ./tmp.mri_nu_correct.mni.72906/output.mean.dat sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.72906/ones.mgz Loading ./tmp.mri_nu_correct.mni.72906/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.72906/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.72906/nu2.mnc ./tmp.mri_nu_correct.mni.72906/nu2.mnc mul .96339522148081033593 Saving result to './tmp.mri_nu_correct.mni.72906/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.72906/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.72906/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.72906/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 13 seconds. mapping ( 8, 164) to ( 3, 110) Wed Jan 27 12:36:00 EST 2016 mri_nu_correct.mni done \n mri_add_xform_to_header -c /space/freesurfer/subjects/test/bert.Darwin/mri/transforms/talairach.xfm nu.mgz nu.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed Jan 27 12:36:03 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_normalize -g 1 nu.mgz T1.mgz \n using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.10650 -0.01792 0.03738 -5.92123; 0.01876 0.97218 0.13882 -22.78761; -0.04190 -0.16861 1.10422 -2.21724; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 80 (80), valley at 58 (58) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 80 (80), valley at 44 (44) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 56 seconds. #-------------------------------------------- #@# Skull Stripping Wed Jan 27 12:39:02 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_em_register -skull nu.mgz /usr/local/freesurfer/dev/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta \n aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/dev/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (49, 46, 10) --> (204, 255, 206) using (101, 116, 108) as brain centroid... mean wm in atlas = 118, using box (82,90,84) --> (120, 141,132) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 109 +- 0.1 after smoothing, mri peak at 109, scaling input intensities by 1.083 scaling channel 0 by 1.08257 initial log_p = -4.169 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.230140 @ (0.000, 0.000, 0.000) max log p = -4.230140 @ (0.000, 0.000, 0.000) max log p = -4.174992 @ (-2.273, -2.273, -6.818) max log p = -4.159032 @ (1.136, 1.136, 1.136) max log p = -4.155935 @ (0.568, 0.568, 0.568) max log p = -4.155935 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -0.6, -5.1): log p = -4.156 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.013, old_max_log_p =-4.156 (thresh=-4.2) 1.05465 0.13705 0.02041 -27.39928; -0.15011 1.12538 0.16757 -16.57227; 0.00000 -0.10324 0.92177 17.00657; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.005, old_max_log_p =-4.013 (thresh=-4.0) 1.14511 -0.01184 -0.00176 -17.32996; -0.01116 1.13364 0.16880 -35.46367; 0.00000 -0.10324 0.92177 17.00657; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.005, old_max_log_p =-4.005 (thresh=-4.0) 1.14511 -0.01184 -0.00176 -17.32996; -0.01116 1.13364 0.16880 -35.46367; 0.00000 -0.10324 0.92177 17.00657; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.941, old_max_log_p =-4.005 (thresh=-4.0) 1.12188 0.02486 0.00268 -21.45131; -0.04767 1.11422 0.13469 -22.57145; -0.00036 -0.06875 0.94397 11.98531; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.941, old_max_log_p =-3.941 (thresh=-3.9) 1.12188 0.02486 0.00268 -21.45131; -0.04767 1.11422 0.13469 -22.57145; -0.00036 -0.06875 0.94397 11.98531; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.928, old_max_log_p =-3.941 (thresh=-3.9) 1.12486 0.01580 0.00152 -20.09089; -0.03843 1.11248 0.14224 -24.38762; 0.00003 -0.07780 0.94173 13.33121; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.926, old_max_log_p =-3.928 (thresh=-3.9) 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.926 (old=-4.169) transform before final EM align: 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 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: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.12797 -0.00242 -0.00056 -17.95047; -0.02003 1.11502 0.12697 -26.30820; -0.00059 -0.05944 0.94172 10.15064; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... registration took 16 minutes and 41 seconds. \n mri_watershed -T1 -brain_atlas /usr/local/freesurfer/dev/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n 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=130 y=112 z=118 r=88 first estimation of the main basin volume: 2949319 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=111, y=97, z=76, Imax=255 CSF=14, 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=2812163904718413 voxels, voxel volume =1.000 = 2812163904718413 mmm3 = 2812163928358.912 cm3 done. PostAnalyze...Basin Prior 65 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=121, z=107, r=10258 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=3, CSF_MAX=17 , nb = 43532 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=62 , nb = 1089312493 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=33 , nb = -1069330044 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=16 , nb = -1034876726 LEFT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=15 , nb = 18837 OTHER CSF_MIN=0, CSF_intensity=32, CSF_MAX=45 , nb = 1090519454 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 17, 33, 59, 80 after analyzing : 17, 50, 59, 57 RIGHT_CER before analyzing : 62, 59, 59, 88 after analyzing : 32, 59, 59, 66 LEFT_CER before analyzing : 33, 56, 70, 88 after analyzing : 33, 65, 70, 70 RIGHT_BRAIN before analyzing : 16, 30, 57, 80 after analyzing : 16, 48, 57, 56 LEFT_BRAIN before analyzing : 15, 32, 60, 79 after analyzing : 15, 50, 60, 57 OTHER before analyzing : 45, 34, 21, 39 after analyzing : 33, 34, 34, 35 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 71.469, std = 9.316 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.37, sigma = 3.50 after rotation: sse = 2.37, sigma = 3.50 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.37, its var is 2.73 before Erosion-Dilatation 0.00% 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...50 iterations mri_strip_skull: done peeling brain Brain Size = 1810015 voxels, voxel volume = 1.000 mm3 = 1810015 mmm3 = 1810.015 cm3 ****************************** Saving brainmask.auto.mgz done \n cp brainmask.auto.mgz brainmask.mgz \n #------------------------------------- #@# EM Registration Wed Jan 27 12:56:25 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca transforms/talairach.lta \n setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca'... average std = 7.4 using min determinant for regularization = 5.4 0 singular and 937 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.2 or > 452.2 total sample mean = 78.8 (1019 zeros) ************************************************ spacing=8, using 2854 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2854, passno 0, spacing 8 resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (65, 59, 25) --> (191, 181, 206) using (107, 100, 116) as brain centroid... mean wm in atlas = 105, using box (92,85,94) --> (122, 114,138) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 0.1 after smoothing, mri peak at 108, scaling input intensities by 0.972 scaling channel 0 by 0.972222 initial log_p = -3.780 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.705969 @ (0.000, 0.000, 0.000) max log p = -3.705969 @ (0.000, 0.000, 0.000) max log p = -3.662482 @ (-2.273, 2.273, -2.273) max log p = -3.650745 @ (-1.136, -1.136, 1.136) max log p = -3.611758 @ (-0.568, 0.568, -2.841) max log p = -3.611758 @ (0.000, 0.000, 0.000) Found translation: (-4.0, 1.7, -4.0): log p = -3.612 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.534, old_max_log_p =-3.612 (thresh=-3.6) 1.15000 0.00000 0.00000 -23.73236; 0.00000 1.05465 0.10263 -16.10925; 0.00000 -0.15011 0.84273 31.20377; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.534, old_max_log_p =-3.534 (thresh=-3.5) 1.15000 0.00000 0.00000 -23.73236; 0.00000 1.05465 0.10263 -16.10925; 0.00000 -0.15011 0.84273 31.20377; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.372, old_max_log_p =-3.534 (thresh=-3.5) 1.12703 -0.00638 0.02901 -21.08113; 0.00000 1.10893 0.13756 -26.53522; -0.03622 -0.19135 0.86991 39.62160; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.372, old_max_log_p =-3.372 (thresh=-3.4) 1.12703 -0.00638 0.02901 -21.08113; 0.00000 1.10893 0.13756 -26.53522; -0.03622 -0.19135 0.86991 39.62160; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.347, old_max_log_p =-3.372 (thresh=-3.4) 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.347, old_max_log_p =-3.347 (thresh=-3.3) 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2854 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; nsamples 2854 Quasinewton: input matrix 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 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: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.347 (old=-3.780) transform before final EM align: 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 314792 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; nsamples 314792 Quasinewton: input matrix 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 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) = 3.9 tol 0.000000 final transform: 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... registration took 12 minutes and 22 seconds. #-------------------------------------- #@# CA Normalize Wed Jan 27 13:08:48 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca transforms/talairach.lta norm.mgz \n writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (64, 58, 25) --> (191, 181, 207) using (106, 99, 116) as brain centroid... mean wm in atlas = 105, using box (90,84,94) --> (121, 114,138) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 0.1 after smoothing, mri peak at 108, scaling input intensities by 0.972 scaling channel 0 by 0.972222 using 245868 sample points... INFO: compute sample coordinates transform 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44823; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (128, 60, 22) --> (187, 161, 209) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 175.0 2 of 9245 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (71, 61, 21) --> (129, 162, 209) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 175.0 5 of 8870 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (130, 139, 55) --> (172, 177, 114) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 175.0 1 of 405 (0.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (89, 140, 51) --> (129, 176, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 175.0 0 of 185 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (113, 129, 93) --> (144, 191, 127) Brain_Stem: limiting intensities to 84.0 --> 175.0 0 of 807 (0.0%) samples deleted using 19512 total control points for intensity normalization... bias field = 0.981 +- 0.046 84 of 19504 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (128, 60, 22) --> (187, 161, 209) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 161.0 3 of 9435 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (71, 61, 21) --> (129, 162, 209) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 161.0 2 of 9044 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (130, 139, 55) --> (172, 177, 114) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 161.0 0 of 412 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (89, 140, 51) --> (129, 176, 114) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 161.0 0 of 194 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (113, 129, 93) --> (144, 191, 127) Brain_Stem: limiting intensities to 78.0 --> 161.0 0 of 877 (0.0%) samples deleted using 19962 total control points for intensity normalization... bias field = 1.037 +- 0.039 79 of 19877 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (128, 60, 22) --> (187, 161, 209) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 161.0 5 of 9448 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (71, 61, 21) --> (129, 162, 209) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 161.0 4 of 9039 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (130, 139, 55) --> (172, 177, 114) Left_Cerebellum_White_Matter: limiting intensities to 77.0 --> 161.0 16 of 443 (3.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (89, 140, 51) --> (129, 176, 114) Right_Cerebellum_White_Matter: limiting intensities to 75.0 --> 161.0 11 of 217 (5.1%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (113, 129, 93) --> (144, 191, 127) Brain_Stem: limiting intensities to 75.0 --> 161.0 0 of 883 (0.0%) samples deleted using 20030 total control points for intensity normalization... bias field = 1.031 +- 0.034 88 of 19847 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 50 seconds. #-------------------------------------- #@# CA Reg Wed Jan 27 13:10:40 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca transforms/talairach.m3z \n 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... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.12 (predicted orig area = 7.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.821, neg=0, invalid=3294 0001: dt=221.952000, rms=0.754 (8.208%), neg=0, invalid=3294 0002: dt=201.394495, rms=0.729 (3.360%), neg=0, invalid=3294 0003: dt=130.433460, rms=0.720 (1.174%), neg=0, invalid=3294 0004: dt=295.936000, rms=0.713 (0.987%), neg=0, invalid=3294 0005: dt=110.976000, rms=0.709 (0.498%), neg=0, invalid=3294 0006: dt=517.888000, rms=0.705 (0.595%), neg=0, invalid=3294 0007: dt=110.976000, rms=0.703 (0.324%), neg=0, invalid=3294 0008: dt=517.888000, rms=0.700 (0.358%), neg=0, invalid=3294 0009: dt=110.976000, rms=0.698 (0.269%), neg=0, invalid=3294 0010: dt=443.904000, rms=0.697 (0.222%), neg=0, invalid=3294 0011: dt=443.904000, rms=0.697 (-1.461%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=3294 0012: dt=153.142857, rms=0.692 (0.707%), neg=0, invalid=3294 0013: dt=221.952000, rms=0.691 (0.239%), neg=0, invalid=3294 0014: dt=221.952000, rms=0.690 (0.148%), neg=0, invalid=3294 0015: dt=221.952000, rms=0.687 (0.336%), neg=0, invalid=3294 0016: dt=221.952000, rms=0.686 (0.261%), neg=0, invalid=3294 0017: dt=221.952000, rms=0.683 (0.396%), neg=0, invalid=3294 0018: dt=221.952000, rms=0.681 (0.272%), neg=0, invalid=3294 0019: dt=221.952000, rms=0.679 (0.356%), neg=0, invalid=3294 0020: dt=221.952000, rms=0.677 (0.233%), neg=0, invalid=3294 0021: dt=221.952000, rms=0.675 (0.263%), neg=0, invalid=3294 0022: dt=221.952000, rms=0.674 (0.242%), neg=0, invalid=3294 0023: dt=221.952000, rms=0.672 (0.238%), neg=0, invalid=3294 0024: dt=221.952000, rms=0.670 (0.266%), neg=0, invalid=3294 0025: dt=221.952000, rms=0.669 (0.213%), neg=0, invalid=3294 0026: dt=221.952000, rms=0.667 (0.259%), neg=0, invalid=3294 0027: dt=221.952000, rms=0.666 (0.185%), neg=0, invalid=3294 0028: dt=221.952000, rms=0.665 (0.177%), neg=0, invalid=3294 0029: dt=221.952000, rms=0.664 (0.122%), neg=0, invalid=3294 0030: dt=221.952000, rms=0.663 (0.129%), neg=0, invalid=3294 0031: dt=221.952000, rms=0.662 (0.141%), neg=0, invalid=3294 0032: dt=221.952000, rms=0.661 (0.105%), neg=0, invalid=3294 0033: dt=221.952000, rms=0.661 (0.142%), neg=0, invalid=3294 0034: dt=221.952000, rms=0.660 (0.124%), neg=0, invalid=3294 0035: dt=221.952000, rms=0.659 (0.113%), neg=0, invalid=3294 0036: dt=92.480000, rms=0.659 (0.020%), neg=0, invalid=3294 0037: dt=92.480000, rms=0.659 (0.008%), neg=0, invalid=3294 0038: dt=92.480000, rms=0.659 (0.018%), neg=0, invalid=3294 0039: dt=92.480000, rms=0.658 (0.026%), neg=0, invalid=3294 0040: dt=92.480000, rms=0.658 (0.028%), neg=0, invalid=3294 0041: dt=92.480000, rms=0.658 (0.036%), neg=0, invalid=3294 0042: dt=92.480000, rms=0.658 (0.035%), neg=0, invalid=3294 0043: dt=92.480000, rms=0.658 (0.032%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.666, neg=0, invalid=3294 0044: dt=36.288000, rms=0.664 (0.317%), neg=0, invalid=3294 0045: dt=169.316456, rms=0.660 (0.632%), neg=0, invalid=3294 0046: dt=235.969466, rms=0.648 (1.860%), neg=0, invalid=3294 0047: dt=31.104000, rms=0.645 (0.511%), neg=0, invalid=3294 0048: dt=15.552000, rms=0.644 (0.018%), neg=0, invalid=3294 0049: dt=15.552000, rms=0.644 (0.023%), neg=0, invalid=3294 0050: dt=15.552000, rms=0.644 (-0.010%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=3294 0051: dt=157.866667, rms=0.639 (0.965%), neg=0, invalid=3294 0052: dt=36.288000, rms=0.637 (0.331%), neg=0, invalid=3294 0053: dt=145.152000, rms=0.635 (0.274%), neg=0, invalid=3294 0054: dt=145.152000, rms=0.632 (0.386%), neg=0, invalid=3294 0055: dt=36.288000, rms=0.631 (0.173%), neg=0, invalid=3294 0056: dt=36.288000, rms=0.631 (0.046%), neg=0, invalid=3294 0057: dt=36.288000, rms=0.630 (0.094%), neg=0, invalid=3294 0058: dt=36.288000, rms=0.629 (0.163%), neg=0, invalid=3294 0059: dt=36.288000, rms=0.628 (0.250%), neg=0, invalid=3294 0060: dt=36.288000, rms=0.626 (0.263%), neg=0, invalid=3294 0061: dt=36.288000, rms=0.625 (0.258%), neg=0, invalid=3294 0062: dt=36.288000, rms=0.624 (0.031%), neg=0, invalid=3294 0063: dt=36.288000, rms=0.624 (0.097%), neg=0, invalid=3294 0064: dt=18.144000, rms=0.624 (0.029%), neg=0, invalid=3294 0065: dt=0.567000, rms=0.624 (0.000%), neg=0, invalid=3294 0066: dt=0.567000, rms=0.624 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.646, neg=0, invalid=3294 0067: dt=2.800000, rms=0.645 (0.236%), neg=0, invalid=3294 0068: dt=2.400000, rms=0.644 (0.096%), neg=0, invalid=3294 0069: dt=0.037500, rms=0.644 (0.003%), neg=0, invalid=3294 0070: dt=0.018750, rms=0.644 (0.001%), neg=0, invalid=3294 0071: dt=0.009375, rms=0.644 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=3294 0072: dt=0.007812, rms=0.644 (0.118%), neg=0, invalid=3294 0073: dt=0.000684, rms=0.644 (0.000%), neg=0, invalid=3294 0074: dt=0.000342, rms=0.644 (0.000%), neg=0, invalid=3294 0075: dt=0.000085, rms=0.644 (0.000%), neg=0, invalid=3294 0076: dt=0.000085, rms=0.644 (0.000%), neg=0, invalid=3294 0077: dt=0.000005, rms=0.644 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.710, neg=0, invalid=3294 0078: dt=8.764105, rms=0.686 (3.361%), neg=0, invalid=3294 0079: dt=3.812500, rms=0.685 (0.090%), neg=0, invalid=3294 0080: dt=3.812500, rms=0.685 (0.116%), neg=0, invalid=3294 0081: dt=3.812500, rms=0.684 (0.117%), neg=0, invalid=3294 0082: dt=3.812500, rms=0.684 (-0.060%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=3294 0083: dt=0.000000, rms=0.684 (0.089%), neg=0, invalid=3294 0084: dt=0.000000, rms=0.684 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.741, neg=0, invalid=3294 0085: dt=0.000000, rms=0.741 (0.075%), neg=0, invalid=3294 0086: dt=0.000000, rms=0.741 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.741, neg=0, invalid=3294 0087: dt=0.064000, rms=0.741 (0.077%), neg=0, invalid=3294 0088: dt=0.028000, rms=0.741 (-0.000%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.645, neg=0, invalid=3294 0089: dt=0.320000, rms=0.635 (1.501%), neg=0, invalid=3294 0090: dt=0.000000, rms=0.635 (-0.000%), neg=0, invalid=3294 0091: dt=0.050000, rms=0.635 (-0.117%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.636, neg=0, invalid=3294 0092: dt=0.000000, rms=0.635 (0.101%), neg=0, invalid=3294 0093: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=3294 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12974 (17) mri peak = 0.16322 (27) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1552 voxels, overlap=0.332) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1552 voxels, peak = 25), gca=25.4 gca peak = 0.13808 (16) mri peak = 0.18391 (30) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (1395 voxels, overlap=0.090) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1395 voxels, peak = 29), gca=24.0 gca peak = 0.25042 (96) mri peak = 0.10980 (93) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1020 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1020 voxels, peak = 95), gca=94.6 gca peak = 0.22986 (96) mri peak = 0.08994 (95) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (932 voxels, overlap=0.985) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (932 voxels, peak = 98), gca=98.4 gca peak = 0.21624 (56) mri peak = 0.07943 (72) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1093 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1093 voxels, peak = 69), gca=68.6 gca peak = 0.29672 (58) mri peak = 0.07588 (76) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1107 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1107 voxels, peak = 73), gca=73.4 gca peak = 0.11066 (101) mri peak = 0.15133 (103) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (81274 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (81274 voxels, peak = 105), gca=104.5 gca peak = 0.10944 (101) mri peak = 0.17106 (103) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84250 voxels, overlap=0.611) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84250 voxels, peak = 105), gca=104.5 gca peak = 0.14864 (59) mri peak = 0.04885 (77) Left_Cerebral_Cortex (3): linear fit = 1.32 x + 0.0 (56720 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.32 x + 0.0 (56720 voxels, peak = 78), gca=77.6 gca peak = 0.16234 (58) mri peak = 0.04832 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (59416 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (59416 voxels, peak = 78), gca=78.0 gca peak = 0.14764 (67) mri peak = 0.13559 (82) Right_Caudate (50): linear fit = 1.22 x + 0.0 (672 voxels, overlap=0.023) Right_Caudate (50): linear fit = 1.22 x + 0.0 (672 voxels, peak = 81), gca=81.4 gca peak = 0.15152 (71) mri peak = 0.11584 (77) Left_Caudate (11): linear fit = 1.05 x + 0.0 (997 voxels, overlap=0.471) Left_Caudate (11): linear fit = 1.05 x + 0.0 (997 voxels, peak = 75), gca=74.9 gca peak = 0.12476 (59) mri peak = 0.05272 (80) Left_Cerebellum_Cortex (8): linear fit = 1.39 x + 0.0 (28278 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.39 x + 0.0 (28278 voxels, peak = 82), gca=82.3 gca peak = 0.13886 (58) mri peak = 0.04294 (82) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (28203 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (28203 voxels, peak = 81), gca=81.5 gca peak = 0.19332 (88) mri peak = 0.11540 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (10005 voxels, overlap=0.593) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (10005 voxels, peak = 95), gca=95.5 gca peak = 0.19182 (87) mri peak = 0.05471 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8043 voxels, overlap=0.987) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8043 voxels, peak = 93), gca=92.7 gca peak = 0.19349 (58) mri peak = 0.12296 (77) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (516 voxels, overlap=0.058) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (516 voxels, peak = 75), gca=74.5 gca peak = 0.32581 (57) mri peak = 0.10266 (75) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (532 voxels, overlap=0.038) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (532 voxels, peak = 75), gca=75.0 gca peak = 0.09144 (86) mri peak = 0.08706 (92) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5639 voxels, overlap=0.722) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5639 voxels, peak = 92), gca=91.6 gca peak = 0.10273 (84) mri peak = 0.09636 (92) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4891 voxels, overlap=0.600) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4891 voxels, peak = 91), gca=91.1 gca peak = 0.13860 (78) mri peak = 0.07654 (88) Left_Putamen (12): linear fit = 1.13 x + 0.0 (2863 voxels, overlap=0.494) Left_Putamen (12): linear fit = 1.13 x + 0.0 (2863 voxels, peak = 89), gca=88.5 gca peak = 0.12691 (78) mri peak = 0.08276 (88) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2744 voxels, overlap=0.686) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2744 voxels, peak = 87), gca=87.0 gca peak = 0.11764 (82) mri peak = 0.13089 (89) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12079 voxels, overlap=0.343) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12079 voxels, peak = 90), gca=89.8 gca peak = 0.10015 (86) mri peak = 0.11177 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1402 voxels, overlap=0.401) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1402 voxels, peak = 93), gca=93.3 gca peak = 0.11151 (90) mri peak = 0.10223 (96) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1771 voxels, overlap=0.328) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1771 voxels, peak = 97), gca=96.8 gca peak = 0.19608 (23) mri peak = 1.00000 (27) gca peak = 0.13512 (19) mri peak = 0.17647 (27) Fourth_Ventricle (15): linear fit = 1.34 x + 0.0 (721 voxels, overlap=0.336) Fourth_Ventricle (15): linear fit = 1.34 x + 0.0 (721 voxels, peak = 25), gca=25.4 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.12743 (29) gca peak Left_Thalamus = 0.71074 (95) gca peak Third_Ventricle = 0.19608 (23) gca peak CSF = 0.17789 (37) gca peak Left_Accumbens_area = 0.50032 (62) gca peak Left_undetermined = 0.97690 (28) gca peak Left_vessel = 0.36001 (53) gca peak Left_choroid_plexus = 0.12300 (45) gca peak Right_Inf_Lat_Vent = 0.21149 (25) gca peak Right_Accumbens_area = 0.31737 (65) gca peak Right_vessel = 0.50186 (52) gca peak Right_choroid_plexus = 0.10991 (44) gca peak Fifth_Ventricle = 0.55462 (35) gca peak WM_hypointensities = 0.10555 (76) gca peak non_WM_hypointensities = 0.08508 (48) gca peak Optic_Chiasm = 0.30852 (73) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.29 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.44 x + 0.0 saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.636, neg=0, invalid=3294 0094: dt=80.795322, rms=0.616 (3.150%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0095: dt=141.736585, rms=0.611 (0.718%), neg=0, invalid=3294 0096: dt=517.888000, rms=0.601 (1.726%), neg=0, invalid=3294 0097: dt=23.120000, rms=0.601 (0.020%), neg=0, invalid=3294 0098: dt=23.120000, rms=0.601 (0.007%), neg=0, invalid=3294 0099: dt=23.120000, rms=0.601 (-0.015%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=3294 0100: dt=443.904000, rms=0.595 (0.994%), neg=0, invalid=3294 0101: dt=110.976000, rms=0.595 (0.083%), neg=0, invalid=3294 0102: dt=110.976000, rms=0.594 (0.094%), neg=0, invalid=3294 0103: dt=110.976000, rms=0.593 (0.134%), neg=0, invalid=3294 0104: dt=110.976000, rms=0.592 (0.173%), neg=0, invalid=3294 0105: dt=110.976000, rms=0.591 (0.229%), neg=0, invalid=3294 0106: dt=110.976000, rms=0.589 (0.248%), neg=0, invalid=3294 0107: dt=110.976000, rms=0.588 (0.247%), neg=0, invalid=3294 0108: dt=110.976000, rms=0.587 (0.234%), neg=0, invalid=3294 0109: dt=110.976000, rms=0.585 (0.220%), neg=0, invalid=3294 0110: dt=110.976000, rms=0.584 (0.202%), neg=0, invalid=3294 0111: dt=110.976000, rms=0.583 (0.193%), neg=0, invalid=3294 0112: dt=110.976000, rms=0.582 (0.192%), neg=0, invalid=3294 0113: dt=110.976000, rms=0.581 (0.192%), neg=0, invalid=3294 0114: dt=110.976000, rms=0.580 (0.171%), neg=0, invalid=3294 0115: dt=110.976000, rms=0.579 (0.146%), neg=0, invalid=3294 0116: dt=110.976000, rms=0.578 (0.132%), neg=0, invalid=3294 0117: dt=110.976000, rms=0.577 (0.124%), neg=0, invalid=3294 0118: dt=110.976000, rms=0.577 (0.108%), neg=0, invalid=3294 0119: dt=443.904000, rms=0.576 (0.057%), neg=0, invalid=3294 0120: dt=443.904000, rms=0.576 (-0.188%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=3294 0121: dt=79.186441, rms=0.576 (0.461%), neg=0, invalid=3294 0122: dt=253.184603, rms=0.565 (1.917%), neg=0, invalid=3294 0123: dt=31.104000, rms=0.563 (0.313%), neg=0, invalid=3294 0124: dt=36.288000, rms=0.563 (0.064%), neg=0, invalid=3294 0125: dt=36.288000, rms=0.562 (0.115%), neg=0, invalid=3294 0126: dt=36.288000, rms=0.561 (0.225%), neg=0, invalid=3294 0127: dt=36.288000, rms=0.559 (0.331%), neg=0, invalid=3294 0128: dt=36.288000, rms=0.557 (0.416%), neg=0, invalid=3294 0129: dt=36.288000, rms=0.554 (0.436%), neg=0, invalid=3294 0130: dt=36.288000, rms=0.552 (0.392%), neg=0, invalid=3294 0131: dt=36.288000, rms=0.550 (0.325%), neg=0, invalid=3294 0132: dt=36.288000, rms=0.549 (0.247%), neg=0, invalid=3294 0133: dt=36.288000, rms=0.548 (0.200%), neg=0, invalid=3294 0134: dt=36.288000, rms=0.547 (0.181%), neg=0, invalid=3294 0135: dt=36.288000, rms=0.546 (0.177%), neg=0, invalid=3294 0136: dt=36.288000, rms=0.545 (0.199%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1000 iterations, nbhd size=8, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.502320: new neg 1, old_neg 1, delta 0, rms=0.002 (3.087%) iter 2, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.083%) iter 3, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.076%) iter 4, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.070%) iter 5, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.064%) iter 6, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.059%) iter 7, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.055%) iter 8, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.051%) iter 9, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.048%) iter 10, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.045%) iter 11, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.042%) iter 12, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.039%) iter 13, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.037%) iter 14, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.035%) iter 15, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.034%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.032%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.031%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.029%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.028%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.027%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.025%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.025%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.015%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.015%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.015%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.015%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.015%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 51, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 52, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 53, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 54, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 55, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 56, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.014%) iter 57, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 58, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 59, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 60, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 61, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 62, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 63, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 64, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 65, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 66, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.013%) iter 67, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 68, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 69, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 70, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 71, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 72, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 73, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 74, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 75, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 76, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 77, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 78, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 79, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 80, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 81, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 82, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.012%) iter 83, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 84, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 85, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 86, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 87, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 88, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 89, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 90, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 91, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 92, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 93, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 94, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 95, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 96, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 97, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 98, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 99, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) iter 100, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.011%) ---------- unfolding failed - restoring original position -------------------- 0137: dt=36.288000, rms=0.545 (-0.004%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1000 iterations, nbhd size=8, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.541325: new neg 1, old_neg 1, delta 0, rms=0.002 (3.109%) iter 2, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.086%) iter 3, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.080%) iter 4, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.073%) iter 5, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.068%) iter 6, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.063%) iter 7, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.059%) iter 8, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.055%) iter 9, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.051%) iter 10, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.048%) iter 11, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.046%) iter 12, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.043%) iter 13, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.041%) iter 14, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.039%) iter 15, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.038%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.036%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.035%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.034%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.032%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.031%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.031%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.030%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.029%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.028%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.028%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.027%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.025%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.025%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 51, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 52, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 53, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 54, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 55, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 56, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 57, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 58, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 59, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 60, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 61, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 62, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 63, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 64, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 65, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 66, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 67, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 68, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 69, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 70, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 71, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 72, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 73, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 74, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 75, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 76, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 77, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 78, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 79, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 80, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 81, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 82, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 83, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 84, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 85, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 86, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 87, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 88, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 89, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 90, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 91, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 92, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 93, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 94, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 95, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 96, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 97, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 98, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 99, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 100, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) ---------- unfolding failed - restoring original position -------------------- 0138: dt=124.416000, rms=0.545 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1000 iterations, nbhd size=8, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.547850: new neg 1, old_neg 1, delta 0, rms=0.002 (2.823%) iter 2, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.069%) iter 3, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.064%) iter 4, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.059%) iter 5, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.055%) iter 6, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.051%) iter 7, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.048%) iter 8, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.045%) iter 9, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.042%) iter 10, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.040%) iter 11, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.038%) iter 12, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.036%) iter 13, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.035%) iter 14, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.033%) iter 15, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.032%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.031%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.030%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.029%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.028%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.027%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.025%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 51, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 52, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 53, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 54, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 55, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 56, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 57, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 58, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 59, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 60, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 61, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 62, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 63, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 64, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 65, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 66, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 67, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 68, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 69, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 70, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 71, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 72, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 73, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 74, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 75, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 76, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 77, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 78, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 79, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 80, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 81, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 82, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 83, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 84, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 85, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 86, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 87, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 88, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 89, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 90, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 91, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 92, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 93, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 94, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 95, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 96, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 97, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 98, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 99, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 100, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) ---------- unfolding failed - restoring original position -------------------- 0139: dt=124.216749, rms=0.545 (0.059%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1000 iterations, nbhd size=8, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.547850: new neg 1, old_neg 1, delta 0, rms=0.002 (2.823%) iter 2, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.069%) iter 3, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.064%) iter 4, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.059%) iter 5, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.055%) iter 6, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.051%) iter 7, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.048%) iter 8, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.045%) iter 9, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.042%) iter 10, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.040%) iter 11, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.038%) iter 12, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.036%) iter 13, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.035%) iter 14, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.033%) iter 15, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.032%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.031%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.030%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.029%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.028%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.027%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.026%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.025%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.024%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.023%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.022%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.021%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.020%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.019%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.018%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 51, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 52, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 53, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 54, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 55, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 56, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 57, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 58, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 59, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.017%) iter 60, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 61, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 62, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 63, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 64, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 65, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 66, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 67, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 68, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 69, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 70, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 71, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 72, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 73, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 74, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 75, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 76, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 77, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 78, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 79, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 80, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 81, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 82, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 83, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 84, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 85, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 86, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 87, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 88, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 89, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 90, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 91, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 92, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 93, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 94, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 95, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 96, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 97, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 98, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 99, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) iter 100, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.002 (0.016%) ---------- unfolding failed - restoring original position -------------------- 0140: dt=124.216749, rms=0.545 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.560, neg=0, invalid=3294 0141: dt=31.055199, rms=0.555 (1.001%), neg=0, invalid=3294 0142: dt=62.730159, rms=0.551 (0.570%), neg=0, invalid=3294 0143: dt=38.400000, rms=0.550 (0.249%), neg=0, invalid=3294 0144: dt=38.400000, rms=0.548 (0.360%), neg=0, invalid=3294 0145: dt=38.400000, rms=0.546 (0.376%), neg=0, invalid=3294 0146: dt=38.400000, rms=0.545 (0.201%), neg=0, invalid=3294 0147: dt=38.400000, rms=0.543 (0.308%), neg=0, invalid=3294 0148: dt=38.400000, rms=0.541 (0.319%), neg=0, invalid=3294 0149: dt=38.400000, rms=0.541 (0.165%), neg=0, invalid=3294 0150: dt=38.400000, rms=0.540 (0.048%), neg=0, invalid=3294 0151: dt=38.400000, rms=0.540 (0.118%), neg=0, invalid=3294 0152: dt=38.400000, rms=0.539 (0.132%), neg=0, invalid=3294 0153: dt=38.400000, rms=0.539 (0.046%), neg=0, invalid=3294 0154: dt=38.400000, rms=0.539 (-0.017%), neg=0, invalid=3294 0155: dt=11.200000, rms=0.539 (0.012%), neg=0, invalid=3294 0156: dt=1.600000, rms=0.539 (0.002%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=3294 0157: dt=24.638498, rms=0.538 (0.211%), neg=0, invalid=3294 0158: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=3294 0159: dt=0.250000, rms=0.538 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.558, neg=0, invalid=3294 0160: dt=0.000000, rms=0.557 (0.049%), neg=0, invalid=3294 0161: dt=0.000000, rms=0.557 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.558, neg=0, invalid=3294 0162: dt=0.000000, rms=0.557 (0.049%), neg=0, invalid=3294 0163: dt=0.000000, rms=0.557 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.597, neg=0, invalid=3294 0164: dt=0.849154, rms=0.589 (1.381%), neg=0, invalid=3294 0165: dt=0.384000, rms=0.588 (0.086%), neg=0, invalid=3294 0166: dt=0.384000, rms=0.588 (-0.013%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=3294 0167: dt=0.384000, rms=0.588 (0.124%), neg=0, invalid=3294 0168: dt=0.112000, rms=0.588 (0.011%), neg=0, invalid=3294 0169: dt=0.112000, rms=0.588 (0.005%), neg=0, invalid=3294 0170: dt=0.112000, rms=0.588 (-0.006%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.557, neg=0, invalid=3294 0171: dt=0.719577, rms=0.544 (2.370%), neg=0, invalid=3294 0172: dt=0.048000, rms=0.543 (0.081%), neg=0, invalid=3294 0173: dt=0.048000, rms=0.543 (-0.040%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=3294 0174: dt=0.024000, rms=0.543 (0.074%), neg=0, invalid=3294 0175: dt=0.000010, rms=0.543 (-0.000%), neg=0, invalid=3294 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.536, neg=0, invalid=3294 0176: dt=0.000000, rms=0.536 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.536, neg=0, invalid=3294 0177: dt=295.936000, rms=0.535 (0.223%), neg=0, invalid=3294 0178: dt=295.936000, rms=0.533 (0.256%), neg=0, invalid=3294 0179: dt=92.480000, rms=0.533 (0.047%), neg=0, invalid=3294 0180: dt=92.480000, rms=0.533 (0.022%), neg=0, invalid=3294 0181: dt=92.480000, rms=0.533 (0.041%), neg=0, invalid=3294 0182: dt=92.480000, rms=0.533 (0.062%), neg=0, invalid=3294 0183: dt=92.480000, rms=0.532 (0.081%), neg=0, invalid=3294 0184: dt=92.480000, rms=0.532 (0.085%), neg=0, invalid=3294 0185: dt=92.480000, rms=0.531 (0.073%), neg=0, invalid=3294 0186: dt=92.480000, rms=0.531 (0.058%), neg=0, invalid=3294 0187: dt=517.888000, rms=0.531 (0.025%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.531, neg=0, invalid=3294 0188: dt=36.288000, rms=0.530 (0.141%), neg=0, invalid=3294 0189: dt=145.152000, rms=0.527 (0.547%), neg=0, invalid=3294 0190: dt=331.776000, rms=0.520 (1.477%), neg=0, invalid=3294 0191: dt=21.194805, rms=0.519 (0.120%), neg=0, invalid=3294 0192: dt=21.194805, rms=0.519 (-0.011%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=3294 0193: dt=117.413534, rms=0.517 (0.356%), neg=0, invalid=3294 0194: dt=124.416000, rms=0.516 (0.307%), neg=0, invalid=3294 0195: dt=36.288000, rms=0.515 (0.088%), neg=0, invalid=3294 0196: dt=36.288000, rms=0.515 (0.035%), neg=0, invalid=3294 0197: dt=36.288000, rms=0.515 (0.054%), neg=0, invalid=3294 0198: dt=36.288000, rms=0.514 (0.081%), neg=0, invalid=3294 0199: dt=36.288000, rms=0.514 (0.116%), neg=0, invalid=3294 0200: dt=36.288000, rms=0.513 (0.128%), neg=0, invalid=3294 0201: dt=36.288000, rms=0.512 (0.124%), neg=0, invalid=3294 0202: dt=36.288000, rms=0.512 (0.117%), neg=0, invalid=3294 0203: dt=103.680000, rms=0.512 (0.018%), neg=0, invalid=3294 0204: dt=103.680000, rms=0.511 (0.079%), neg=0, invalid=3294 0205: dt=103.680000, rms=0.511 (0.079%), neg=0, invalid=3294 0206: dt=103.680000, rms=0.510 (0.082%), neg=0, invalid=3294 0207: dt=103.680000, rms=0.510 (0.144%), neg=0, invalid=3294 0208: dt=103.680000, rms=0.509 (0.160%), neg=0, invalid=3294 0209: dt=103.680000, rms=0.508 (0.140%), neg=0, invalid=3294 0210: dt=103.680000, rms=0.507 (0.142%), neg=0, invalid=3294 0211: dt=103.680000, rms=0.507 (0.163%), neg=0, invalid=3294 0212: dt=103.680000, rms=0.506 (0.133%), neg=0, invalid=3294 0213: dt=103.680000, rms=0.505 (0.110%), neg=0, invalid=3294 0214: dt=103.680000, rms=0.505 (0.114%), neg=0, invalid=3294 0215: dt=103.680000, rms=0.504 (0.105%), neg=0, invalid=3294 0216: dt=0.005062, rms=0.504 (0.000%), neg=0, invalid=3294 0217: dt=0.005062, rms=0.504 (-0.000%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=3294 0218: dt=2.800000, rms=0.509 (0.011%), neg=0, invalid=3294 0219: dt=2.800000, rms=0.509 (0.006%), neg=0, invalid=3294 0220: dt=2.800000, rms=0.509 (0.002%), neg=0, invalid=3294 0221: dt=2.800000, rms=0.509 (-0.015%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=3294 0222: dt=11.200000, rms=0.509 (0.053%), neg=0, invalid=3294 0223: dt=8.000000, rms=0.509 (0.013%), neg=0, invalid=3294 0224: dt=8.000000, rms=0.509 (0.006%), neg=0, invalid=3294 0225: dt=8.000000, rms=0.509 (-0.017%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=3294 0226: dt=1.857143, rms=0.519 (0.063%), neg=0, invalid=3294 0227: dt=0.063000, rms=0.519 (0.000%), neg=0, invalid=3294 0228: dt=0.063000, rms=0.519 (0.000%), neg=0, invalid=3294 0229: dt=0.063000, rms=0.519 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=3294 0230: dt=0.864000, rms=0.519 (0.009%), neg=0, invalid=3294 0231: dt=0.144000, rms=0.519 (0.000%), neg=0, invalid=3294 0232: dt=0.144000, rms=0.519 (-0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.535, neg=0, invalid=3294 0233: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=3294 0234: dt=0.256000, rms=0.535 (0.023%), neg=0, invalid=3294 0235: dt=0.080000, rms=0.535 (0.002%), neg=0, invalid=3294 0236: dt=0.080000, rms=0.535 (-0.001%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=3294 0237: dt=0.653631, rms=0.501 (2.000%), neg=0, invalid=3294 0238: dt=0.028000, rms=0.501 (0.034%), neg=0, invalid=3294 0239: dt=0.028000, rms=0.501 (-0.009%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.501, neg=0, invalid=3294 0240: dt=0.024000, rms=0.501 (0.013%), neg=0, invalid=3294 0241: dt=0.000000, rms=0.501 (0.000%), neg=0, invalid=3294 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 48 minutes and 13 seconds. FSRUNTIME@ mri_ca_register 3.8035 hours 1 threads #-------------------------------------- #@# Remove Neck Wed Jan 27 16:58:54 EST 2016 \n mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca nu_noneck.mgz \n erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 7.16 removing structures at least 25 mm from brain... 11026155 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 11 seconds. #-------------------------------------- #@# SubCort Seg Wed Jan 27 17:00:07 EST 2016 \n mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz \n sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /space/freesurfer/subjects/test cd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca... reading input volume from norm.mgz... average std[0] = 7.4 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 7.16 Atlas used for the 3D morph was /usr/local/freesurfer/dev/average/RB_all_2015-08-04.gca average std = 7.4 using min determinant for regularization = 5.4 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16337 (20) mri peak = 0.17417 (28) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (1679 voxels, overlap=0.231) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (1679 voxels, peak = 27), gca=27.1 gca peak = 0.19190 (13) mri peak = 0.16890 (30) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (1384 voxels, overlap=0.103) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1384 voxels, peak = 27), gca=19.5 gca peak = 0.24200 (96) mri peak = 0.12903 (96) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (820 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (820 voxels, peak = 97), gca=97.4 gca peak = 0.14904 (91) mri peak = 0.13383 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (807 voxels, overlap=0.921) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (807 voxels, peak = 94), gca=94.2 gca peak = 0.25211 (57) mri peak = 0.08593 (72) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1014 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1014 voxels, peak = 73), gca=72.7 gca peak = 0.31987 (57) mri peak = 0.09559 (74) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1090 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1090 voxels, peak = 72), gca=71.5 gca peak = 0.08094 (102) mri peak = 0.15535 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (64305 voxels, overlap=0.600) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (64305 voxels, peak = 103), gca=102.5 gca peak = 0.08600 (104) mri peak = 0.17855 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (64300 voxels, overlap=0.588) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (64300 voxels, peak = 104), gca=104.0 gca peak = 0.09612 (57) mri peak = 0.05203 (78) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (62444 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (62444 voxels, peak = 77), gca=76.7 gca peak = 0.11462 (58) mri peak = 0.05607 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (59379 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (59379 voxels, peak = 78), gca=78.0 gca peak = 0.25255 (66) mri peak = 0.15694 (82) Right_Caudate (50): linear fit = 1.21 x + 0.0 (813 voxels, overlap=0.019) Right_Caudate (50): linear fit = 1.21 x + 0.0 (813 voxels, peak = 80), gca=79.5 gca peak = 0.18480 (77) mri peak = 0.15432 (77) Left_Caudate (11): linear fit = 1.02 x + 0.0 (815 voxels, overlap=0.518) Left_Caudate (11): linear fit = 1.02 x + 0.0 (815 voxels, peak = 79), gca=78.9 gca peak = 0.12729 (58) mri peak = 0.06457 (80) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (31297 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (31297 voxels, peak = 80), gca=80.3 gca peak = 0.12622 (58) mri peak = 0.06132 (80) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (32134 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (32134 voxels, peak = 80), gca=80.3 gca peak = 0.15410 (88) mri peak = 0.14858 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8359 voxels, overlap=0.487) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8359 voxels, peak = 94), gca=93.7 gca peak = 0.15661 (88) mri peak = 0.11313 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7643 voxels, overlap=0.445) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7643 voxels, peak = 95), gca=95.5 gca peak = 0.30376 (59) mri peak = 0.10034 (72) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (588 voxels, overlap=0.046) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (588 voxels, peak = 75), gca=75.2 gca peak = 0.35132 (58) mri peak = 0.11822 (76) Right_Amygdala (54): linear fit = 1.34 x + 0.0 (513 voxels, overlap=0.041) Right_Amygdala (54): linear fit = 1.34 x + 0.0 (513 voxels, peak = 77), gca=77.4 gca peak = 0.10548 (89) mri peak = 0.09854 (92) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5278 voxels, overlap=0.810) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5278 voxels, peak = 92), gca=92.1 gca peak = 0.10706 (82) mri peak = 0.10250 (92) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5218 voxels, overlap=0.574) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5218 voxels, peak = 90), gca=89.8 gca peak = 0.08512 (74) mri peak = 0.09058 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2310 voxels, overlap=0.492) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2310 voxels, peak = 83), gca=82.5 gca peak = 0.08440 (78) mri peak = 0.10511 (88) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2112 voxels, overlap=0.422) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2112 voxels, peak = 87), gca=87.0 gca peak = 0.07263 (80) mri peak = 0.11394 (89) Brain_Stem (16): linear fit = 1.08 x + 0.0 (15979 voxels, overlap=0.490) Brain_Stem (16): linear fit = 1.08 x + 0.0 (15979 voxels, peak = 86), gca=86.0 gca peak = 0.13309 (90) mri peak = 0.10865 (96) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1939 voxels, overlap=0.387) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1939 voxels, peak = 96), gca=95.9 gca peak = 0.15558 (86) mri peak = 0.11261 (95) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (2058 voxels, overlap=0.459) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (2058 voxels, peak = 92), gca=92.5 gca peak = 0.17913 (26) mri peak = 0.26667 (26) gca peak = 0.17310 (16) mri peak = 0.15033 (26) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (290 voxels, overlap=0.243) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (290 voxels, peak = 25), gca=25.4 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.21424 (27) gca peak Left_Thalamus = 1.00000 (95) gca peak Third_Ventricle = 0.17913 (26) gca peak Fourth_Ventricle = 0.17310 (16) gca peak CSF = 0.22008 (37) gca peak Left_Accumbens_area = 0.78455 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09096 (57) gca peak Right_Inf_Lat_Vent = 0.24233 (28) gca peak Right_Accumbens_area = 0.41783 (64) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11536 (37) gca peak Fifth_Ventricle = 0.55384 (33) gca peak WM_hypointensities = 0.10945 (75) gca peak non_WM_hypointensities = 0.07381 (29) gca peak Optic_Chiasm = 0.66945 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.30 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.43 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12143 (27) mri peak = 0.17417 (28) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1679 voxels, overlap=0.677) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1679 voxels, peak = 27), gca=26.6 gca peak = 0.14450 (19) mri peak = 0.16890 (30) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (1384 voxels, overlap=0.260) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (1384 voxels, peak = 27), gca=26.5 gca peak = 0.21116 (98) mri peak = 0.12903 (96) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (820 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (820 voxels, peak = 97), gca=96.5 gca peak = 0.15623 (99) mri peak = 0.13383 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (807 voxels, overlap=0.998) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (807 voxels, peak = 99), gca=99.0 gca peak = 0.21676 (72) mri peak = 0.08593 (72) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1014 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1014 voxels, peak = 71), gca=70.9 gca peak = 0.28523 (72) mri peak = 0.09559 (74) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1090 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1090 voxels, peak = 73), gca=73.1 gca peak = 0.08259 (104) mri peak = 0.15535 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (64305 voxels, overlap=0.616) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (64305 voxels, peak = 104), gca=104.0 gca peak = 0.08600 (104) mri peak = 0.17855 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (64300 voxels, overlap=0.588) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (64300 voxels, peak = 104), gca=104.0 gca peak = 0.07365 (78) mri peak = 0.05203 (78) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (62444 voxels, overlap=0.793) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (62444 voxels, peak = 76), gca=76.1 gca peak = 0.08305 (78) mri peak = 0.05607 (79) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (59379 voxels, overlap=0.886) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (59379 voxels, peak = 77), gca=76.8 gca peak = 0.23064 (80) mri peak = 0.15694 (82) Right_Caudate (50): linear fit = 0.99 x + 0.0 (813 voxels, overlap=0.997) Right_Caudate (50): linear fit = 0.99 x + 0.0 (813 voxels, peak = 79), gca=78.8 gca peak = 0.21432 (79) mri peak = 0.15432 (77) Left_Caudate (11): linear fit = 1.00 x + 0.0 (815 voxels, overlap=0.599) Left_Caudate (11): linear fit = 1.00 x + 0.0 (815 voxels, peak = 79), gca=79.0 gca peak = 0.09401 (80) mri peak = 0.06457 (80) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (31297 voxels, overlap=0.912) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (31297 voxels, peak = 79), gca=78.8 gca peak = 0.09624 (80) mri peak = 0.06132 (80) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32134 voxels, overlap=0.915) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32134 voxels, peak = 79), gca=78.8 gca peak = 0.15843 (94) mri peak = 0.14858 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8359 voxels, overlap=0.888) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8359 voxels, peak = 94), gca=93.5 gca peak = 0.14207 (94) mri peak = 0.11313 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7643 voxels, overlap=0.912) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7643 voxels, peak = 94), gca=93.5 gca peak = 0.29512 (75) mri peak = 0.10034 (72) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (588 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (588 voxels, peak = 75), gca=75.0 gca peak = 0.25732 (77) mri peak = 0.11822 (76) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (513 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (513 voxels, peak = 77), gca=77.0 gca peak = 0.10992 (92) mri peak = 0.09854 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5278 voxels, overlap=0.915) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5278 voxels, peak = 92), gca=91.5 gca peak = 0.11627 (90) mri peak = 0.10250 (92) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5218 voxels, overlap=0.904) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5218 voxels, peak = 91), gca=91.3 gca peak = 0.07078 (84) mri peak = 0.09058 (89) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2310 voxels, overlap=0.893) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2310 voxels, peak = 85), gca=85.3 gca peak = 0.08236 (84) mri peak = 0.10511 (88) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2112 voxels, overlap=0.893) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2112 voxels, peak = 84), gca=84.0 gca peak = 0.07173 (87) mri peak = 0.11394 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (15979 voxels, overlap=0.737) Brain_Stem (16): linear fit = 1.00 x + 0.0 (15979 voxels, peak = 87), gca=87.0 gca peak = 0.13348 (90) mri peak = 0.10865 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1939 voxels, overlap=0.786) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1939 voxels, peak = 90), gca=90.0 gca peak = 0.14593 (93) mri peak = 0.11261 (95) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2058 voxels, overlap=0.862) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2058 voxels, peak = 93), gca=93.0 gca peak = 0.12796 (37) mri peak = 0.26667 (26) gca peak = 0.12399 (26) mri peak = 0.15033 (26) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (290 voxels, overlap=0.646) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (290 voxels, peak = 29), gca=29.0 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.17508 (34) gca peak Left_Thalamus = 0.35898 (124) gca peak Third_Ventricle = 0.12796 (37) gca peak CSF = 0.19510 (53) gca peak Left_Accumbens_area = 0.38729 (64) gca peak Left_undetermined = 0.97815 (31) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09968 (44) gca peak Right_Inf_Lat_Vent = 0.29639 (30) gca peak Right_Accumbens_area = 0.37092 (78) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11438 (37) gca peak Fifth_Ventricle = 0.55752 (44) gca peak WM_hypointensities = 0.10333 (75) gca peak non_WM_hypointensities = 0.08016 (44) gca peak Optic_Chiasm = 0.65232 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.17 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 85443 voxels changed in iteration 0 of unlikely voxel relabeling 318 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 83537 gm and wm labels changed (%35 to gray, %65 to white out of all changed labels) 439 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 71581 changed. image ll: -2.216, PF=0.500 pass 2: 21375 changed. image ll: -2.215, PF=0.500 pass 3: 6758 changed. pass 4: 2625 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 40 minutes and 8 seconds. \n mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /space/freesurfer/subjects/test/bert.Darwin/mri/transforms/cc_up.lta bert.Darwin \n will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /space/freesurfer/subjects/test/bert.Darwin/mri/transforms/cc_up.lta reading aseg from /space/freesurfer/subjects/test/bert.Darwin/mri/aseg.auto_noCCseg.mgz reading norm from /space/freesurfer/subjects/test/bert.Darwin/mri/norm.mgz 41368 voxels in left wm, 58319 in right wm, xrange [123, 133] searching rotation angles z=[-10 4], y=[-7 7] searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 global minimum found at slice 128.3, rotations (0.33, -3.10) final transformation (x=128.3, yr=0.334, zr=-3.105): 0.99852 0.05416 0.00582 -6.26974; -0.05416 0.99853 -0.00032 34.13454; -0.00583 -0.00000 0.99998 17.74967; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 101 111 eigenvectors: 0.00127 -0.00187 1.00000; -0.01548 -0.99988 -0.00185; 0.99988 -0.01548 -0.00129; writing aseg with callosum to /space/freesurfer/subjects/test/bert.Darwin/mri/aseg.auto.mgz... corpus callosum segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Wed Jan 27 17:41:20 EST 2016 \n cp aseg.auto.mgz aseg.presurf.mgz \n #-------------------------------------------- #@# Intensity Normalization2 Wed Jan 27 17:41:21 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz \n using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 930 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 84 (84), valley at 57 (57) csf peak at 37, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 40 (40) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 19 seconds. #-------------------------------------------- #@# Mask BFS Wed Jan 27 17:45:44 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 DoAbs = 0 Found 1726265 voxels in mask (pct= 10.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jan 27 17:45:48 EST 2016 \n mri_segment brain.mgz wm.seg.mgz \n doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.8 +- 5.9 [80.0 --> 125.0] GM (80.0) : 77.7 +- 12.8 [30.0 --> 96.0] setting bottom of white matter range to 90.5 setting top of gray matter range to 103.3 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... 6678 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3921 filled 9201 bright non-wm voxels segmented. 3490 diagonally connected voxels added... white matter segmentation took 2.2 minutes writing output to wm.seg.mgz... \n mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz \n preserving editing changes in input volume... auto filling took 0.65 minutes reading wm segmentation from wm.seg.mgz... 143 voxels added to wm to prevent paths from MTL structures to cortex 4544 additional wm voxels added 0 additional wm voxels added SEG EDIT: 51161 voxels turned on, 49846 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.... \n mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz \n Iteration Number : 1 pass 1 (xy+): 19 found - 19 modified | TOTAL: 19 pass 2 (xy+): 0 found - 19 modified | TOTAL: 19 pass 1 (xy-): 14 found - 14 modified | TOTAL: 33 pass 2 (xy-): 0 found - 14 modified | TOTAL: 33 pass 1 (yz+): 33 found - 33 modified | TOTAL: 66 pass 2 (yz+): 0 found - 33 modified | TOTAL: 66 pass 1 (yz-): 35 found - 35 modified | TOTAL: 101 pass 2 (yz-): 0 found - 35 modified | TOTAL: 101 pass 1 (xz+): 11 found - 11 modified | TOTAL: 112 pass 2 (xz+): 0 found - 11 modified | TOTAL: 112 pass 1 (xz-): 14 found - 14 modified | TOTAL: 126 pass 2 (xz-): 0 found - 14 modified | TOTAL: 126 Iteration Number : 1 pass 1 (+++): 16 found - 16 modified | TOTAL: 16 pass 2 (+++): 0 found - 16 modified | TOTAL: 16 pass 1 (+++): 17 found - 17 modified | TOTAL: 33 pass 2 (+++): 0 found - 17 modified | TOTAL: 33 pass 1 (+++): 6 found - 6 modified | TOTAL: 39 pass 2 (+++): 0 found - 6 modified | TOTAL: 39 pass 1 (+++): 3 found - 3 modified | TOTAL: 42 pass 2 (+++): 0 found - 3 modified | TOTAL: 42 Iteration Number : 1 pass 1 (++): 56 found - 56 modified | TOTAL: 56 pass 2 (++): 0 found - 56 modified | TOTAL: 56 pass 1 (+-): 73 found - 73 modified | TOTAL: 129 pass 2 (+-): 0 found - 73 modified | TOTAL: 129 pass 1 (--): 78 found - 78 modified | TOTAL: 207 pass 2 (--): 0 found - 78 modified | TOTAL: 207 pass 1 (-+): 67 found - 67 modified | TOTAL: 274 pass 2 (-+): 0 found - 67 modified | TOTAL: 274 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 6 found - 6 modified | TOTAL: 11 pass 2 (yz+): 0 found - 6 modified | TOTAL: 11 pass 1 (yz-): 6 found - 6 modified | TOTAL: 17 pass 2 (yz-): 0 found - 6 modified | TOTAL: 17 pass 1 (xz+): 5 found - 5 modified | TOTAL: 22 pass 2 (xz+): 0 found - 5 modified | TOTAL: 22 pass 1 (xz-): 3 found - 3 modified | TOTAL: 25 pass 2 (xz-): 0 found - 3 modified | TOTAL: 25 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 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 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 2 found - 2 modified | TOTAL: 9 pass 2 (-+): 0 found - 2 modified | TOTAL: 9 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 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 (++): 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 : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 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 : 5 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 : 5 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 = 488 (out of 573971: 0.085022) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Jan 27 17:48:46 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz \n 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 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44822; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.12555 0.01175 0.03122 -22.82080; -0.01838 1.10499 0.13658 -24.50938; -0.03634 -0.19202 0.87297 38.44822; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1017 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (126, 105, 119), TAL = (2.0, -9.0, 23.0) talairach voxel to voxel transform 0.88726 -0.01455 -0.02946 21.02389; 0.00992 0.88087 -0.13817 27.12845; 0.03912 0.19315 1.11389 -37.20030; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 105, 119) --> (2.0, -9.0, 23.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (2.00, -9.00, 23.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -9.00, 23.00) SRC: (111.81, 104.25, 119.86) search lh wm seed point around talairach space (-16.00, -9.00, 23.00), SRC: (143.76, 104.61, 121.27) 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 Wed Jan 27 17:49:39 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz \n Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 276747: 0.001807) Ambiguous edge configurations... mri_pretess done \n mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix \n $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ slice 30: 511 vertices, 575 faces slice 40: 4519 vertices, 4709 faces slice 50: 11264 vertices, 11520 faces slice 60: 19445 vertices, 19760 faces slice 70: 29166 vertices, 29510 faces slice 80: 39106 vertices, 39426 faces slice 90: 48663 vertices, 49022 faces slice 100: 59628 vertices, 60009 faces slice 110: 70093 vertices, 70504 faces slice 120: 80509 vertices, 80910 faces slice 130: 90689 vertices, 91101 faces slice 140: 100300 vertices, 100666 faces slice 150: 108045 vertices, 108339 faces slice 160: 114207 vertices, 114519 faces slice 170: 120703 vertices, 120984 faces slice 180: 126586 vertices, 126831 faces slice 190: 131311 vertices, 131516 faces slice 200: 134565 vertices, 134682 faces slice 210: 134818 vertices, 134888 faces slice 220: 134818 vertices, 134888 faces slice 230: 134818 vertices, 134888 faces slice 240: 134818 vertices, 134888 faces slice 250: 134818 vertices, 134888 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; \n rm -f ../mri/filled-pretess255.mgz \n \n mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix \n counting number of connected components... 134818 voxel in cpt #1: X=-70 [v=134818,e=404664,f=269776] located at (-26.657124, -19.603718, 15.181110) For the whole surface: X=-70 [v=134818,e=404664,f=269776] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Jan 27 17:49:49 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz \n Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 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 : 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 = 4 (out of 276090: 0.001449) Ambiguous edge configurations... mri_pretess done \n mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix \n $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ slice 30: 632 vertices, 717 faces slice 40: 4387 vertices, 4560 faces slice 50: 11328 vertices, 11593 faces slice 60: 19831 vertices, 20129 faces slice 70: 29919 vertices, 30291 faces slice 80: 39963 vertices, 40290 faces slice 90: 49992 vertices, 50361 faces slice 100: 61186 vertices, 61589 faces slice 110: 71242 vertices, 71645 faces slice 120: 81596 vertices, 81993 faces slice 130: 90900 vertices, 91282 faces slice 140: 99748 vertices, 100074 faces slice 150: 106703 vertices, 106987 faces slice 160: 112715 vertices, 112993 faces slice 170: 119260 vertices, 119538 faces slice 180: 125174 vertices, 125436 faces slice 190: 130039 vertices, 130261 faces slice 200: 133429 vertices, 133553 faces slice 210: 133832 vertices, 133898 faces slice 220: 133832 vertices, 133898 faces slice 230: 133832 vertices, 133898 faces slice 240: 133832 vertices, 133898 faces slice 250: 133832 vertices, 133898 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; \n rm -f ../mri/filled-pretess127.mgz \n \n mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix \n counting number of connected components... 133832 voxel in cpt #1: X=-66 [v=133832,e=401694,f=267796] located at (26.270945, -20.204592, 17.942226) For the whole surface: X=-66 [v=133832,e=401694,f=267796] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jan 27 17:49:58 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Wed Jan 27 17:50:11 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Jan 27 17:50:24 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix \n Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.7 mm, total surface area = 72395 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.151 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.038 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Inflation1 rh Wed Jan 27 17:51:08 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix \n Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.9 mm, total surface area = 72359 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.149 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.036 (target=0.015) step 060: RMS=0.035 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Jan 27 17:51:47 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix \n doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.59 (0.00-->6.34) (max @ vno 52488 --> 53609) face area 0.02 +- 0.03 (-0.06-->0.48) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.808, avgs=0 005/300: dt: 0.9000, rms radial error=177.548, avgs=0 010/300: dt: 0.9000, rms radial error=176.988, avgs=0 015/300: dt: 0.9000, rms radial error=176.253, avgs=0 020/300: dt: 0.9000, rms radial error=175.417, avgs=0 025/300: dt: 0.9000, rms radial error=174.523, avgs=0 030/300: dt: 0.9000, rms radial error=173.595, avgs=0 035/300: dt: 0.9000, rms radial error=172.649, avgs=0 040/300: dt: 0.9000, rms radial error=171.696, avgs=0 045/300: dt: 0.9000, rms radial error=170.741, avgs=0 050/300: dt: 0.9000, rms radial error=169.786, avgs=0 055/300: dt: 0.9000, rms radial error=168.834, avgs=0 060/300: dt: 0.9000, rms radial error=167.885, avgs=0 065/300: dt: 0.9000, rms radial error=166.941, avgs=0 070/300: dt: 0.9000, rms radial error=166.002, avgs=0 075/300: dt: 0.9000, rms radial error=165.068, avgs=0 080/300: dt: 0.9000, rms radial error=164.139, avgs=0 085/300: dt: 0.9000, rms radial error=163.216, avgs=0 090/300: dt: 0.9000, rms radial error=162.297, avgs=0 095/300: dt: 0.9000, rms radial error=161.384, avgs=0 100/300: dt: 0.9000, rms radial error=160.475, avgs=0 105/300: dt: 0.9000, rms radial error=159.572, avgs=0 110/300: dt: 0.9000, rms radial error=158.673, avgs=0 115/300: dt: 0.9000, rms radial error=157.779, avgs=0 120/300: dt: 0.9000, rms radial error=156.891, avgs=0 125/300: dt: 0.9000, rms radial error=156.011, avgs=0 130/300: dt: 0.9000, rms radial error=155.135, avgs=0 135/300: dt: 0.9000, rms radial error=154.265, avgs=0 140/300: dt: 0.9000, rms radial error=153.399, avgs=0 145/300: dt: 0.9000, rms radial error=152.538, avgs=0 150/300: dt: 0.9000, rms radial error=151.682, avgs=0 155/300: dt: 0.9000, rms radial error=150.832, avgs=0 160/300: dt: 0.9000, rms radial error=149.986, avgs=0 165/300: dt: 0.9000, rms radial error=149.145, avgs=0 170/300: dt: 0.9000, rms radial error=148.308, avgs=0 175/300: dt: 0.9000, rms radial error=147.476, avgs=0 180/300: dt: 0.9000, rms radial error=146.649, avgs=0 185/300: dt: 0.9000, rms radial error=145.826, avgs=0 190/300: dt: 0.9000, rms radial error=145.007, avgs=0 195/300: dt: 0.9000, rms radial error=144.193, avgs=0 200/300: dt: 0.9000, rms radial error=143.384, avgs=0 205/300: dt: 0.9000, rms radial error=142.578, avgs=0 210/300: dt: 0.9000, rms radial error=141.778, avgs=0 215/300: dt: 0.9000, rms radial error=140.981, avgs=0 220/300: dt: 0.9000, rms radial error=140.189, avgs=0 225/300: dt: 0.9000, rms radial error=139.401, avgs=0 230/300: dt: 0.9000, rms radial error=138.618, avgs=0 235/300: dt: 0.9000, rms radial error=137.839, avgs=0 240/300: dt: 0.9000, rms radial error=137.064, avgs=0 245/300: dt: 0.9000, rms radial error=136.293, avgs=0 250/300: dt: 0.9000, rms radial error=135.527, avgs=0 255/300: dt: 0.9000, rms radial error=134.765, avgs=0 260/300: dt: 0.9000, rms radial error=134.007, avgs=0 265/300: dt: 0.9000, rms radial error=133.254, avgs=0 270/300: dt: 0.9000, rms radial error=132.504, avgs=0 275/300: dt: 0.9000, rms radial error=131.759, avgs=0 280/300: dt: 0.9000, rms radial error=131.018, avgs=0 285/300: dt: 0.9000, rms radial error=130.281, avgs=0 290/300: dt: 0.9000, rms radial error=129.549, avgs=0 295/300: dt: 0.9000, rms radial error=128.820, avgs=0 300/300: dt: 0.9000, rms radial error=128.095, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16052.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2789.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 320.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00691 epoch 4 (K=640.0), pass 1, starting sse = 21.02 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/15 = 0.01217 final distance error %29.31 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours FSRUNTIME@ mris_sphere 0.0713 hours 1 threads #-------------------------------------------- #@# QSphere rh Wed Jan 27 17:56:05 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix \n doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.61 (0.00-->7.55) (max @ vno 55066 --> 56236) face area 0.02 +- 0.03 (-0.25-->0.63) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.790, avgs=0 005/300: dt: 0.9000, rms radial error=177.529, avgs=0 010/300: dt: 0.9000, rms radial error=176.968, avgs=0 015/300: dt: 0.9000, rms radial error=176.232, avgs=0 020/300: dt: 0.9000, rms radial error=175.393, avgs=0 025/300: dt: 0.9000, rms radial error=174.497, avgs=0 030/300: dt: 0.9000, rms radial error=173.570, avgs=0 035/300: dt: 0.9000, rms radial error=172.626, avgs=0 040/300: dt: 0.9000, rms radial error=171.675, avgs=0 045/300: dt: 0.9000, rms radial error=170.722, avgs=0 050/300: dt: 0.9000, rms radial error=169.769, avgs=0 055/300: dt: 0.9000, rms radial error=168.819, avgs=0 060/300: dt: 0.9000, rms radial error=167.873, avgs=0 065/300: dt: 0.9000, rms radial error=166.932, avgs=0 070/300: dt: 0.9000, rms radial error=165.995, avgs=0 075/300: dt: 0.9000, rms radial error=165.063, avgs=0 080/300: dt: 0.9000, rms radial error=164.136, avgs=0 085/300: dt: 0.9000, rms radial error=163.215, avgs=0 090/300: dt: 0.9000, rms radial error=162.298, avgs=0 095/300: dt: 0.9000, rms radial error=161.387, avgs=0 100/300: dt: 0.9000, rms radial error=160.480, avgs=0 105/300: dt: 0.9000, rms radial error=159.579, avgs=0 110/300: dt: 0.9000, rms radial error=158.682, avgs=0 115/300: dt: 0.9000, rms radial error=157.790, avgs=0 120/300: dt: 0.9000, rms radial error=156.903, avgs=0 125/300: dt: 0.9000, rms radial error=156.021, avgs=0 130/300: dt: 0.9000, rms radial error=155.143, avgs=0 135/300: dt: 0.9000, rms radial error=154.271, avgs=0 140/300: dt: 0.9000, rms radial error=153.403, avgs=0 145/300: dt: 0.9000, rms radial error=152.540, avgs=0 150/300: dt: 0.9000, rms radial error=151.681, avgs=0 155/300: dt: 0.9000, rms radial error=150.828, avgs=0 160/300: dt: 0.9000, rms radial error=149.980, avgs=0 165/300: dt: 0.9000, rms radial error=149.137, avgs=0 170/300: dt: 0.9000, rms radial error=148.298, avgs=0 175/300: dt: 0.9000, rms radial error=147.464, avgs=0 180/300: dt: 0.9000, rms radial error=146.635, avgs=0 185/300: dt: 0.9000, rms radial error=145.810, avgs=0 190/300: dt: 0.9000, rms radial error=144.990, avgs=0 195/300: dt: 0.9000, rms radial error=144.174, avgs=0 200/300: dt: 0.9000, rms radial error=143.363, avgs=0 205/300: dt: 0.9000, rms radial error=142.556, avgs=0 210/300: dt: 0.9000, rms radial error=141.754, avgs=0 215/300: dt: 0.9000, rms radial error=140.956, avgs=0 220/300: dt: 0.9000, rms radial error=140.164, avgs=0 225/300: dt: 0.9000, rms radial error=139.377, avgs=0 230/300: dt: 0.9000, rms radial error=138.594, avgs=0 235/300: dt: 0.9000, rms radial error=137.816, avgs=0 240/300: dt: 0.9000, rms radial error=137.042, avgs=0 245/300: dt: 0.9000, rms radial error=136.272, avgs=0 250/300: dt: 0.9000, rms radial error=135.507, avgs=0 255/300: dt: 0.9000, rms radial error=134.745, avgs=0 260/300: dt: 0.9000, rms radial error=133.988, avgs=0 265/300: dt: 0.9000, rms radial error=133.236, avgs=0 270/300: dt: 0.9000, rms radial error=132.487, avgs=0 275/300: dt: 0.9000, rms radial error=131.743, avgs=0 280/300: dt: 0.9000, rms radial error=131.003, avgs=0 285/300: dt: 0.9000, rms radial error=130.267, avgs=0 290/300: dt: 0.9000, rms radial error=129.535, avgs=0 295/300: dt: 0.9000, rms radial error=128.807, avgs=0 300/300: dt: 0.9000, rms radial error=128.083, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15961.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 2 (K=40.0), pass 1, starting sse = 2798.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 3 (K=160.0), pass 1, starting sse = 322.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00464 epoch 4 (K=640.0), pass 1, starting sse = 24.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/13 = 0.01025 final distance error %29.92 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours FSRUNTIME@ mris_sphere 0.0650 hours 1 threads #-------------------------------------------- #@# Fix Topology lh Wed Jan 27 18:00:00 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n #-------------------------------------------- #@# Fix Topology rh Wed Jan 27 18:00:01 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n cp ../surf/rh.orig.nofix ../surf/rh.orig \n \n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 bert.Darwin lh \n 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 1.49 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ before topology correction, eno=-70 (nv=134818, nf=269776, ne=404664, g=36) 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... 3917 ambiguous faces found in tessellation segmenting defects... 46 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 -merging segment 29 into 30 -merging segment 34 into 32 -merging segment 45 into 44 42 defects to be corrected 0 vertices coincident reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6645 (-4.3322) -vertex loglikelihood: -5.5060 (-2.7530) -normal dot loglikelihood: -3.5714 (-3.5714) -quad curv loglikelihood: -6.2818 (-3.1409) Total Loglikelihood : -24.0237 CORRECTING DEFECT 0 (vertices=29, convex hull=69) After retessellation of defect 0, euler #=-42 (132387,396067,263638) : difference with theory (-39) = 3 CORRECTING DEFECT 1 (vertices=30, convex hull=68) After retessellation of defect 1, euler #=-41 (132399,396129,263689) : difference with theory (-38) = 3 CORRECTING DEFECT 2 (vertices=50, convex hull=77) After retessellation of defect 2, euler #=-41 (132426,396247,263780) : difference with theory (-37) = 4 CORRECTING DEFECT 3 (vertices=264, convex hull=112) After retessellation of defect 3, euler #=-40 (132471,396432,263921) : difference with theory (-36) = 4 CORRECTING DEFECT 4 (vertices=16, convex hull=53) After retessellation of defect 4, euler #=-39 (132480,396476,263957) : difference with theory (-35) = 4 CORRECTING DEFECT 5 (vertices=46, convex hull=87) After retessellation of defect 5, euler #=-38 (132513,396613,264062) : difference with theory (-34) = 4 CORRECTING DEFECT 6 (vertices=37, convex hull=78) After retessellation of defect 6, euler #=-37 (132535,396711,264139) : difference with theory (-33) = 4 CORRECTING DEFECT 7 (vertices=17, convex hull=31) After retessellation of defect 7, euler #=-36 (132541,396738,264161) : difference with theory (-32) = 4 CORRECTING DEFECT 8 (vertices=12, convex hull=32) After retessellation of defect 8, euler #=-35 (132543,396755,264177) : difference with theory (-31) = 4 CORRECTING DEFECT 9 (vertices=31, convex hull=22) After retessellation of defect 9, euler #=-34 (132546,396770,264190) : difference with theory (-30) = 4 CORRECTING DEFECT 10 (vertices=16, convex hull=57) After retessellation of defect 10, euler #=-32 (132551,396806,264223) : difference with theory (-29) = 3 CORRECTING DEFECT 11 (vertices=5, convex hull=20) After retessellation of defect 11, euler #=-31 (132552,396814,264231) : difference with theory (-28) = 3 CORRECTING DEFECT 12 (vertices=44, convex hull=71) After retessellation of defect 12, euler #=-30 (132568,396889,264291) : difference with theory (-27) = 3 CORRECTING DEFECT 13 (vertices=5, convex hull=23) After retessellation of defect 13, euler #=-29 (132570,396901,264302) : difference with theory (-26) = 3 CORRECTING DEFECT 14 (vertices=23, convex hull=51) After retessellation of defect 14, euler #=-28 (132581,396955,264346) : difference with theory (-25) = 3 CORRECTING DEFECT 15 (vertices=236, convex hull=60) After retessellation of defect 15, euler #=-27 (132598,397030,264405) : difference with theory (-24) = 3 CORRECTING DEFECT 16 (vertices=5, convex hull=38) After retessellation of defect 16, euler #=-26 (132600,397049,264423) : difference with theory (-23) = 3 CORRECTING DEFECT 17 (vertices=35, convex hull=78) After retessellation of defect 17, euler #=-25 (132622,397146,264499) : difference with theory (-22) = 3 CORRECTING DEFECT 18 (vertices=71, convex hull=91) After retessellation of defect 18, euler #=-24 (132647,397254,264583) : difference with theory (-21) = 3 CORRECTING DEFECT 19 (vertices=42, convex hull=82) After retessellation of defect 19, euler #=-23 (132668,397345,264654) : difference with theory (-20) = 3 CORRECTING DEFECT 20 (vertices=36, convex hull=61) After retessellation of defect 20, euler #=-22 (132691,397440,264727) : difference with theory (-19) = 3 CORRECTING DEFECT 21 (vertices=43, convex hull=97) After retessellation of defect 21, euler #=-21 (132722,397573,264830) : difference with theory (-18) = 3 CORRECTING DEFECT 22 (vertices=37, convex hull=60) After retessellation of defect 22, euler #=-20 (132731,397628,264877) : difference with theory (-17) = 3 CORRECTING DEFECT 23 (vertices=161, convex hull=153) After retessellation of defect 23, euler #=-19 (132801,397905,265085) : difference with theory (-16) = 3 CORRECTING DEFECT 24 (vertices=87, convex hull=44) After retessellation of defect 24, euler #=-18 (132810,397950,265122) : difference with theory (-15) = 3 CORRECTING DEFECT 25 (vertices=9, convex hull=20) After retessellation of defect 25, euler #=-17 (132814,397968,265137) : difference with theory (-14) = 3 CORRECTING DEFECT 26 (vertices=154, convex hull=158) After retessellation of defect 26, euler #=-16 (132838,398113,265259) : difference with theory (-13) = 3 CORRECTING DEFECT 27 (vertices=13, convex hull=26) After retessellation of defect 27, euler #=-15 (132842,398131,265274) : difference with theory (-12) = 3 CORRECTING DEFECT 28 (vertices=121, convex hull=86) After retessellation of defect 28, euler #=-13 (132866,398239,265360) : difference with theory (-11) = 2 CORRECTING DEFECT 29 (vertices=51, convex hull=37) After retessellation of defect 29, euler #=-12 (132880,398294,265402) : difference with theory (-10) = 2 CORRECTING DEFECT 30 (vertices=79, convex hull=73) After retessellation of defect 30, euler #=-10 (132885,398344,265449) : difference with theory (-9) = 1 CORRECTING DEFECT 31 (vertices=31, convex hull=26) After retessellation of defect 31, euler #=-9 (132890,398366,265467) : difference with theory (-8) = 1 CORRECTING DEFECT 32 (vertices=110, convex hull=124) After retessellation of defect 32, euler #=-8 (132920,398514,265586) : difference with theory (-7) = 1 CORRECTING DEFECT 33 (vertices=31, convex hull=49) After retessellation of defect 33, euler #=-7 (132931,398566,265628) : difference with theory (-6) = 1 CORRECTING DEFECT 34 (vertices=80, convex hull=90) After retessellation of defect 34, euler #=-6 (132958,398686,265722) : difference with theory (-5) = 1 CORRECTING DEFECT 35 (vertices=56, convex hull=80) After retessellation of defect 35, euler #=-5 (132968,398752,265779) : difference with theory (-4) = 1 CORRECTING DEFECT 36 (vertices=28, convex hull=67) After retessellation of defect 36, euler #=-4 (132976,398802,265822) : difference with theory (-3) = 1 CORRECTING DEFECT 37 (vertices=30, convex hull=78) After retessellation of defect 37, euler #=-3 (132992,398882,265887) : difference with theory (-2) = 1 CORRECTING DEFECT 38 (vertices=39, convex hull=77) After retessellation of defect 38, euler #=-2 (133002,398940,265936) : difference with theory (-1) = 1 CORRECTING DEFECT 39 (vertices=124, convex hull=59) After retessellation of defect 39, euler #=-1 (133011,398994,265982) : difference with theory (0) = 1 CORRECTING DEFECT 40 (vertices=88, convex hull=39) After retessellation of defect 40, euler #=0 (133015,399024,266009) : difference with theory (1) = 1 CORRECTING DEFECT 41 (vertices=19, convex hull=29) After retessellation of defect 41, euler #=2 (133016,399042,266028) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.09-->9.73) (max @ vno 25606 --> 34228) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.09-->9.73) (max @ vno 25606 --> 34228) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 174 mutations (35.3%), 319 crossovers (64.7%), 168 vertices were eliminated building final representation... 1802 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133016, nf=266028, ne=399042, g=0) writing corrected surface to /space/freesurfer/subjects/test/bert.Darwin/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.9 minutes 0 defective edges removing intersecting faces 000: 234 intersecting 001: 8 intersecting FSRUNTIME@ mris_fix_topology lh 0.3648 hours 1 threads \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 bert.Darwin rh \n 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 1.49 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ before topology correction, eno=-66 (nv=133832, nf=267796, ne=401694, g=34) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 3918 ambiguous faces found in tessellation segmenting defects... 31 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 17 into 15 29 defects to be corrected 0 vertices coincident reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7015 (-4.3508) -vertex loglikelihood: -5.5035 (-2.7518) -normal dot loglikelihood: -3.6137 (-3.6137) -quad curv loglikelihood: -6.2063 (-3.1032) Total Loglikelihood : -24.0251 CORRECTING DEFECT 0 (vertices=71, convex hull=99) After retessellation of defect 0, euler #=-26 (131416,393232,261790) : difference with theory (-26) = 0 CORRECTING DEFECT 1 (vertices=71, convex hull=69) After retessellation of defect 1, euler #=-25 (131445,393347,261877) : difference with theory (-25) = 0 CORRECTING DEFECT 2 (vertices=49, convex hull=85) After retessellation of defect 2, euler #=-24 (131473,393468,261971) : difference with theory (-24) = 0 CORRECTING DEFECT 3 (vertices=49, convex hull=58) After retessellation of defect 3, euler #=-23 (131480,393516,262013) : difference with theory (-23) = 0 CORRECTING DEFECT 4 (vertices=98, convex hull=148) After retessellation of defect 4, euler #=-22 (131549,393790,262219) : difference with theory (-22) = 0 CORRECTING DEFECT 5 (vertices=51, convex hull=82) After retessellation of defect 5, euler #=-21 (131579,393916,262316) : difference with theory (-21) = 0 CORRECTING DEFECT 6 (vertices=59, convex hull=99) After retessellation of defect 6, euler #=-20 (131613,394064,262431) : difference with theory (-20) = 0 CORRECTING DEFECT 7 (vertices=715, convex hull=247) After retessellation of defect 7, euler #=-19 (131634,394256,262603) : difference with theory (-19) = 0 CORRECTING DEFECT 8 (vertices=57, convex hull=88) After retessellation of defect 8, euler #=-18 (131647,394342,262677) : difference with theory (-18) = 0 CORRECTING DEFECT 9 (vertices=15, convex hull=20) After retessellation of defect 9, euler #=-17 (131654,394365,262694) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=9, convex hull=40) After retessellation of defect 10, euler #=-16 (131657,394386,262713) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=8, convex hull=26) After retessellation of defect 11, euler #=-15 (131660,394400,262725) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=9, convex hull=15) After retessellation of defect 12, euler #=-14 (131662,394408,262732) : difference with theory (-14) = 0 CORRECTING DEFECT 13 (vertices=70, convex hull=123) After retessellation of defect 13, euler #=-13 (131684,394525,262828) : difference with theory (-13) = 0 CORRECTING DEFECT 14 (vertices=264, convex hull=194) normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132893 with 3 faces normal vector of length zero at vertex 132835 with 4 faces After retessellation of defect 14, euler #=-11 (131700,394671,262960) : difference with theory (-12) = -1 CORRECTING DEFECT 15 (vertices=33, convex hull=78) After retessellation of defect 15, euler #=-10 (131722,394766,263034) : difference with theory (-11) = -1 CORRECTING DEFECT 16 (vertices=41, convex hull=79) After retessellation of defect 16, euler #=-9 (131739,394850,263102) : difference with theory (-10) = -1 CORRECTING DEFECT 17 (vertices=30, convex hull=51) After retessellation of defect 17, euler #=-8 (131749,394900,263143) : difference with theory (-9) = -1 CORRECTING DEFECT 18 (vertices=89, convex hull=82) After retessellation of defect 18, euler #=-7 (131793,395071,263271) : difference with theory (-8) = -1 CORRECTING DEFECT 19 (vertices=10, convex hull=14) After retessellation of defect 19, euler #=-6 (131794,395080,263280) : difference with theory (-7) = -1 CORRECTING DEFECT 20 (vertices=87, convex hull=89) After retessellation of defect 20, euler #=-5 (131824,395207,263378) : difference with theory (-6) = -1 CORRECTING DEFECT 21 (vertices=64, convex hull=33) After retessellation of defect 21, euler #=-4 (131836,395256,263416) : difference with theory (-5) = -1 CORRECTING DEFECT 22 (vertices=22, convex hull=44) After retessellation of defect 22, euler #=-3 (131838,395278,263437) : difference with theory (-4) = -1 CORRECTING DEFECT 23 (vertices=33, convex hull=64) After retessellation of defect 23, euler #=-2 (131860,395369,263507) : difference with theory (-3) = -1 CORRECTING DEFECT 24 (vertices=82, convex hull=100) After retessellation of defect 24, euler #=-1 (131895,395519,263623) : difference with theory (-2) = -1 CORRECTING DEFECT 25 (vertices=164, convex hull=120) After retessellation of defect 25, euler #=-1 (131915,395642,263726) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=80, convex hull=57) After retessellation of defect 26, euler #=0 (131931,395713,263782) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=71, convex hull=108) After retessellation of defect 27, euler #=1 (131954,395831,263878) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=36, convex hull=67) After retessellation of defect 28, euler #=2 (131968,395898,263932) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.09-->12.88) (max @ vno 108901 --> 116377) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.09-->12.88) (max @ vno 108901 --> 116377) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 110 mutations (31.0%), 245 crossovers (69.0%), 371 vertices were eliminated building final representation... 1864 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=131968, nf=263932, ne=395898, g=0) writing corrected surface to /space/freesurfer/subjects/test/bert.Darwin/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.5 minutes 0 defective edges removing intersecting faces 000: 223 intersecting FSRUNTIME@ mris_fix_topology rh 0.4421 hours 1 threads \n mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 133016 - 399042 + 266028 = 2 --> 0 holes F =2V-4: 266028 = 266032-4 (0) 2E=3F: 798084 = 798084 (0) total defect index = 0 \n mris_euler_number ../surf/rh.orig \n euler # = v-e+f = 2g-2: 131968 - 395898 + 263932 = 2 --> 0 holes F =2V-4: 263932 = 263936-4 (0) 2E=3F: 791796 = 791796 (0) total defect index = 0 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_remove_intersection ../surf/lh.orig ../surf/lh.orig \n intersection removal took 0.00 hours removing intersecting faces 000: 32 intersecting writing corrected surface to ../surf/lh.orig \n rm ../surf/lh.inflated \n /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_remove_intersection ../surf/rh.orig ../surf/rh.orig \n intersection removal took 0.00 hours removing intersecting faces 000: 24 intersecting writing corrected surface to ../surf/rh.orig \n rm ../surf/rh.inflated \n #-------------------------------------------- #@# Make White Surf lh Wed Jan 27 18:48:45 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert.Darwin lh \n only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline 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 1.162 2015/12/10 21:15:02 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/filled.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/brain.finalsurfs.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/../mri/aseg.presurf.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... 18558 bright wm thresholded. 10474 bright non-wm voxels segmented. reading original surface position from /space/freesurfer/subjects/test/bert.Darwin/surf/lh.orig... computing class statistics... border white: 259765 voxels (1.55%) border gray 279898 voxels (1.67%) WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.2 +- 9.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 62.8 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 53.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.03-->3.77) (max @ vno 25606 --> 33241) face area 0.28 +- 0.12 (0.00-->2.88) mean absolute distance = 0.89 +- 1.07 3956 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-2.6, GM=82+-6.1 mean inside = 100.4, mean outside = 88.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.4, 93 (93) missing vertices, mean dist 0.5 [0.7 (%27.3)->0.9 (%72.7))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.12-->4.66) (max @ vno 132640 --> 82220) face area 0.28 +- 0.13 (0.00-->2.93) mean absolute distance = 0.44 +- 0.69 4187 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2191087.5, rms=8.068 001: dt: 0.5000, sse=1437541.9, rms=5.988 (25.784%) 002: dt: 0.5000, sse=1035324.0, rms=4.476 (25.248%) 003: dt: 0.5000, sse=818237.2, rms=3.373 (24.642%) 004: dt: 0.5000, sse=707610.0, rms=2.652 (21.369%) 005: dt: 0.5000, sse=659128.4, rms=2.231 (15.872%) 006: dt: 0.5000, sse=636977.2, rms=2.029 (9.086%) 007: dt: 0.5000, sse=627577.8, rms=1.921 (5.319%) rms = 1.88, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=623468.4, rms=1.877 (2.280%) 009: dt: 0.2500, sse=588736.2, rms=1.340 (28.611%) 010: dt: 0.2500, sse=584856.8, rms=1.269 (5.268%) rms = 1.25, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=583338.0, rms=1.247 (1.722%) rms = 1.23, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=583195.9, rms=1.235 (0.997%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=91.9, 53 (17) missing vertices, mean dist -0.3 [0.5 (%73.1)->0.2 (%26.9))] %73 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=gust., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.11-->4.83) (max @ vno 132640 --> 132645) face area 0.36 +- 0.16 (0.00-->3.64) mean absolute distance = 0.31 +- 0.44 4127 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1043900.2, rms=3.752 013: dt: 0.5000, sse=817912.4, rms=2.305 (38.568%) 014: dt: 0.5000, sse=757427.2, rms=1.729 (24.982%) 015: dt: 0.5000, sse=736076.6, rms=1.483 (14.240%) 016: dt: 0.5000, sse=729494.3, rms=1.421 (4.196%) rms = 1.45, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=717329.3, rms=1.188 (16.354%) 018: dt: 0.2500, sse=731320.7, rms=1.069 (10.006%) rms = 1.04, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=710616.6, rms=1.035 (3.221%) rms = 1.02, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=709415.0, rms=1.021 (1.368%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=93.9, 36 (9) missing vertices, mean dist -0.2 [0.4 (%73.1)->0.2 (%26.9))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=gust., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.06-->5.08) (max @ vno 88113 --> 88114) face area 0.34 +- 0.16 (0.00-->3.71) mean absolute distance = 0.23 +- 0.33 3616 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=849510.8, rms=2.797 021: dt: 0.5000, sse=711991.3, rms=1.513 (45.901%) 022: dt: 0.5000, sse=690559.4, rms=1.229 (18.749%) 023: dt: 0.5000, sse=689409.6, rms=1.179 (4.109%) rms = 1.23, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=677445.9, rms=0.985 (16.449%) 025: dt: 0.2500, sse=677221.1, rms=0.909 (7.679%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=674832.4, rms=0.906 (0.419%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=94.6, 40 (5) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=gust., 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 /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=681083.6, rms=1.281 027: dt: 0.5000, sse=657155.4, rms=0.840 (34.372%) rms = 1.03, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=652743.3, rms=0.743 (11.548%) rms = 0.73, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=654758.4, rms=0.735 (1.171%) rms = 0.73, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=651485.3, rms=0.729 (0.797%) positioning took 0.6 minutes generating cortex label... 3 non-cortical segments detected only using segment with 8193 vertices erasing segment 1 (vno[0] = 95567) erasing segment 2 (vno[0] = 103203) writing cortex label to /space/freesurfer/subjects/test/bert.Darwin/label/lh.cortex.label... writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/lh.curv writing smoothed area to lh.area writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/lh.area vertex spacing 0.89 +- 0.25 (0.04-->5.02) (max @ vno 88113 --> 88114) face area 0.34 +- 0.16 (0.00-->3.63) refinement took 6.4 minutes #-------------------------------------------- #@# Make White Surf rh Wed Jan 27 18:55:08 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert.Darwin rh \n only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline 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 1.162 2015/12/10 21:15:02 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/filled.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/brain.finalsurfs.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/../mri/aseg.presurf.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... 18558 bright wm thresholded. 10474 bright non-wm voxels segmented. reading original surface position from /space/freesurfer/subjects/test/bert.Darwin/surf/rh.orig... computing class statistics... border white: 259765 voxels (1.55%) border gray 279898 voxels (1.67%) WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.2 +- 9.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 63.8 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 54.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.01-->8.61) (max @ vno 55379 --> 55385) face area 0.29 +- 0.13 (0.00-->9.57) mean absolute distance = 0.89 +- 1.05 3768 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-3.5, GM=83+-6.1 mean inside = 100.5, mean outside = 88.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.7, 27 (27) missing vertices, mean dist 0.5 [0.8 (%26.2)->0.9 (%73.8))] %57 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.15-->7.12) (max @ vno 55379 --> 131618) face area 0.29 +- 0.14 (0.00-->7.27) mean absolute distance = 0.45 +- 0.69 4195 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2128140.5, rms=7.915 001: dt: 0.5000, sse=1399688.8, rms=5.865 (25.897%) 002: dt: 0.5000, sse=1014223.4, rms=4.382 (25.286%) 003: dt: 0.5000, sse=804632.5, rms=3.301 (24.678%) 004: dt: 0.5000, sse=698804.6, rms=2.575 (21.991%) 005: dt: 0.5000, sse=648496.6, rms=2.140 (16.906%) 006: dt: 0.5000, sse=626739.2, rms=1.910 (10.746%) 007: dt: 0.5000, sse=618281.4, rms=1.795 (5.980%) 008: dt: 0.5000, sse=613529.0, rms=1.743 (2.931%) rms = 1.72, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=611608.2, rms=1.716 (1.546%) 010: dt: 0.2500, sse=583059.5, rms=1.218 (29.031%) 011: dt: 0.2500, sse=579688.6, rms=1.163 (4.520%) rms = 1.15, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=579347.2, rms=1.152 (0.934%) rms = 1.14, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=578636.2, rms=1.142 (0.897%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=92.2, 61 (14) missing vertices, mean dist -0.3 [0.5 (%72.8)->0.2 (%27.2))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=gust., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.08-->7.15) (max @ vno 55385 --> 57645) face area 0.36 +- 0.17 (0.00-->10.96) mean absolute distance = 0.32 +- 0.44 4190 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1032689.2, rms=3.688 014: dt: 0.5000, sse=812627.7, rms=2.241 (39.240%) 015: dt: 0.5000, sse=756438.8, rms=1.679 (25.051%) 016: dt: 0.5000, sse=734059.8, rms=1.435 (14.533%) 017: dt: 0.5000, sse=727867.3, rms=1.362 (5.084%) rms = 1.38, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=717925.7, rms=1.158 (15.009%) 019: dt: 0.2500, sse=713327.6, rms=1.056 (8.797%) rms = 1.03, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=711855.0, rms=1.029 (2.538%) rms = 1.02, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=711547.6, rms=1.015 (1.359%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.2, 51 (9) missing vertices, mean dist -0.2 [0.4 (%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=gust., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.08-->7.33) (max @ vno 55385 --> 57645) face area 0.35 +- 0.17 (0.00-->10.79) mean absolute distance = 0.23 +- 0.33 3651 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=853539.9, rms=2.809 022: dt: 0.5000, sse=724174.6, rms=1.518 (45.953%) 023: dt: 0.5000, sse=690935.9, rms=1.200 (20.931%) 024: dt: 0.5000, sse=686751.0, rms=1.142 (4.837%) rms = 1.17, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=678883.9, rms=0.972 (14.898%) 026: dt: 0.2500, sse=676566.9, rms=0.905 (6.924%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=675988.5, rms=0.901 (0.370%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.9, 42 (5) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=gust., 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 /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=680078.7, rms=1.266 028: dt: 0.5000, sse=660029.8, rms=0.813 (35.780%) rms = 0.99, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=656241.4, rms=0.733 (9.829%) rms = 0.73, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=653611.1, rms=0.729 (0.601%) rms = 0.72, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=652467.5, rms=0.725 (0.576%) positioning took 0.6 minutes generating cortex label... 4 non-cortical segments detected only using segment with 7340 vertices erasing segment 0 (vno[0] = 36487) erasing segment 2 (vno[0] = 92531) erasing segment 3 (vno[0] = 96783) writing cortex label to /space/freesurfer/subjects/test/bert.Darwin/label/rh.cortex.label... writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/rh.curv writing smoothed area to rh.area writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->7.55) (max @ vno 53264 --> 56503) face area 0.34 +- 0.16 (0.00-->10.62) refinement took 6.4 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jan 27 19:01:34 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm \n 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... #-------------------------------------------- #@# Smooth2 rh Wed Jan 27 19:01:46 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm \n 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 Wed Jan 27 19:01:58 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated \n Reading ../surf/lh.smoothwm avg radius = 48.8 mm, total surface area = 81514 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.169 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.7 minutes #-------------------------------------------- #@# Inflation2 rh Wed Jan 27 19:02:41 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated \n Reading ../surf/rh.smoothwm avg radius = 49.2 mm, total surface area = 81415 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.169 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.6 minutes #-------------------------------------------- #@# Curv .H and .K lh Wed Jan 27 19:03:20 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/surf \n mris_curvature -w lh.white \n total integrated curvature = 3.036*4pi (38.149) --> -2 handles ICI = 137.6, FI = 1460.3, variation=22904.454 writing Gaussian curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/lh.white.K...done. writing mean curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/lh.white.H...done. \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated \n normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 163 vertices thresholded to be in k1 ~ [-0.57 0.38], k2 ~ [-0.14 0.22] total integrated curvature = 0.589*4pi (7.400) --> 0 handles ICI = 1.5, FI = 8.5, variation=150.935 103 vertices thresholded to be in [-0.05 0.01] writing Gaussian curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 93 vertices thresholded to be in [-0.13 0.15] done. writing mean curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/lh.inflated.H...curvature mean = -0.016, std = 0.021 done. #-------------------------------------------- #@# Curv .H and .K rh Wed Jan 27 19:04:43 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/surf \n mris_curvature -w rh.white \n total integrated curvature = 5.228*4pi (65.701) --> -4 handles ICI = 137.7, FI = 1434.3, variation=22555.873 writing Gaussian curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/rh.white.K...done. writing mean curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/rh.white.H...done. \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated \n normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 155 vertices thresholded to be in k1 ~ [-0.20 0.56], k2 ~ [-0.16 0.17] total integrated curvature = 0.559*4pi (7.029) --> 0 handles ICI = 1.4, FI = 8.4, variation=146.606 154 vertices thresholded to be in [-0.05 0.01] writing Gaussian curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 121 vertices thresholded to be in [-0.13 0.20] done. writing mean curvature to /autofs/cluster/freesurfer/subjects/test/bert.Darwin/surf/rh.inflated.H...curvature mean = -0.016, std = 0.021 done. \n#----------------------------------------- #@# Curvature Stats lh Wed Jan 27 19:06:17 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm bert.Darwin lh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert.Darwin/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 246 ] Gb_filter = 0 WARN: S lookup min: -0.531429 WARN: S explicit min: 0.000000 vertex = 507 \n#----------------------------------------- #@# Curvature Stats rh Wed Jan 27 19:06:27 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm bert.Darwin rh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert.Darwin/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 236 ] Gb_filter = 0 WARN: S lookup min: -0.285235 WARN: S explicit min: 0.000000 vertex = 1740 #-------------------------------------------- #@# Sphere lh Wed Jan 27 19:06:35 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere \n setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.274... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=gust., nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.33 pass 1: epoch 2 of 3 starting distance error %20.29 unfolding complete - removing small folds... starting distance error %20.23 removing remaining folds... final distance error %20.24 MRISunfold() return, current seed 1234 -01: dt=0.0000, 83 negative triangles 183: dt=0.9900, 83 negative triangles 184: dt=0.9900, 35 negative triangles 185: dt=0.9900, 34 negative triangles 186: dt=0.9900, 21 negative triangles 187: dt=0.9900, 22 negative triangles 188: dt=0.9900, 16 negative triangles 189: dt=0.9900, 6 negative triangles 190: dt=0.9900, 13 negative triangles 191: dt=0.9900, 8 negative triangles 192: dt=0.9900, 9 negative triangles 193: dt=0.9900, 5 negative triangles 194: dt=0.9900, 4 negative triangles 195: dt=0.9900, 1 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 1 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 1 negative triangles 200: dt=0.9900, 2 negative triangles 201: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.66 hours FSRUNTIME@ mris_sphere 0.6580 hours 1 threads #-------------------------------------------- #@# Sphere rh Wed Jan 27 19:46:05 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere \n setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.273... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=gust., nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.46 pass 1: epoch 2 of 3 starting distance error %20.43 unfolding complete - removing small folds... starting distance error %20.34 removing remaining folds... final distance error %20.36 MRISunfold() return, current seed 1234 -01: dt=0.0000, 103 negative triangles 176: dt=0.9900, 103 negative triangles 177: dt=0.9900, 54 negative triangles 178: dt=0.9900, 38 negative triangles 179: dt=0.9900, 39 negative triangles 180: dt=0.9900, 36 negative triangles 181: dt=0.9900, 21 negative triangles 182: dt=0.9900, 17 negative triangles 183: dt=0.9900, 13 negative triangles 184: dt=0.9900, 10 negative triangles 185: dt=0.9900, 11 negative triangles 186: dt=0.9900, 14 negative triangles 187: dt=0.9900, 10 negative triangles 188: dt=0.9900, 8 negative triangles 189: dt=0.9900, 5 negative triangles 190: dt=0.9900, 6 negative triangles 191: dt=0.9900, 7 negative triangles 192: dt=0.9900, 3 negative triangles 193: dt=0.9900, 3 negative triangles 194: dt=0.9900, 2 negative triangles 195: dt=0.9900, 4 negative triangles 196: dt=0.9900, 2 negative triangles 197: dt=0.9900, 5 negative triangles 198: dt=0.9900, 2 negative triangles 199: dt=0.9900, 2 negative triangles 200: dt=0.9900, 1 negative triangles 201: dt=0.9900, 1 negative triangles 202: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.64 hours FSRUNTIME@ mris_sphere 0.6388 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Wed Jan 27 20:24:25 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg \n using smoothwm curvature for final alignment cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=gust., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=gust., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 0.594 curvature mean = 0.025, std = 0.932 curvature mean = 0.015, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 301560.0, tmin=1.1680 d=32.00 min @ (8.00, 8.00, 8.00) sse = 270427.8, tmin=2.3640 d=16.00 min @ (-4.00, -4.00, -4.00) sse = 235164.9, tmin=3.5905 d=8.00 min @ (0.00, 2.00, 2.00) sse = 230030.0, tmin=4.8637 d=4.00 min @ (0.00, -1.00, -1.00) sse = 228381.9, tmin=6.1553 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 227851.0, tmin=7.4503 d=1.00 min @ (0.25, 0.25, -0.25) sse = 227669.2, tmin=8.7281 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 227640.5, tmin=9.9945 tol=1.0e+00, sigma=0.5, host=gust., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.99 min curvature mean = 0.010, std = 0.961 curvature mean = 0.007, std = 0.942 curvature mean = 0.009, std = 0.974 curvature mean = 0.003, std = 0.975 curvature mean = 0.009, std = 0.977 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.022, std = 0.267 curvature mean = 0.004, std = 0.067 curvature mean = 0.048, std = 0.380 curvature mean = 0.004, std = 0.080 curvature mean = 0.020, std = 0.581 curvature mean = 0.004, std = 0.086 curvature mean = 0.011, std = 0.720 curvature mean = 0.005, std = 0.090 curvature mean = 0.003, std = 0.824 MRISregister() return, current seed 0 -01: dt=0.0000, 17 negative triangles 113: dt=0.9900, 17 negative triangles 114: dt=0.9900, 16 negative triangles 115: dt=0.9900, 12 negative triangles 116: dt=0.9900, 11 negative triangles 117: dt=0.9900, 4 negative triangles 118: dt=0.9900, 5 negative triangles 119: dt=0.9900, 2 negative triangles 120: dt=0.9900, 1 negative triangles 121: dt=0.9900, 4 negative triangles 122: dt=0.9900, 3 negative triangles 123: dt=0.9900, 1 negative triangles 124: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.71 hours FSRUNTIME@ mris_register 0.7109 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Wed Jan 27 21:07:06 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg \n using smoothwm curvature for final alignment cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=gust., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=gust., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 0.599 curvature mean = 0.028, std = 0.933 curvature mean = 0.019, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 390897.2, tmin=1.1535 d=32.00 min @ (8.00, 8.00, 8.00) sse = 295652.6, tmin=2.3350 d=16.00 min @ (0.00, -4.00, 0.00) sse = 280178.3, tmin=3.5412 d=2.00 min @ (0.50, 0.00, 0.00) sse = 279847.6, tmin=7.1650 d=1.00 min @ (-0.25, 0.00, -0.25) sse = 279829.0, tmin=8.3804 d=0.50 min @ (0.12, 0.12, 0.00) sse = 279785.5, tmin=9.6268 tol=1.0e+00, sigma=0.5, host=gust., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.63 min curvature mean = 0.003, std = 0.952 curvature mean = 0.008, std = 0.943 curvature mean = 0.002, std = 0.962 curvature mean = 0.004, std = 0.975 curvature mean = 0.000, std = 0.963 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.026, std = 0.270 curvature mean = 0.006, std = 0.070 curvature mean = 0.059, std = 0.376 curvature mean = 0.006, std = 0.084 curvature mean = 0.028, std = 0.571 curvature mean = 0.006, std = 0.090 curvature mean = 0.016, std = 0.709 curvature mean = 0.006, std = 0.093 curvature mean = 0.005, std = 0.811 MRISregister() return, current seed 0 -01: dt=0.0000, 154 negative triangles 114: dt=0.9900, 154 negative triangles expanding nbhd size to 1 115: dt=0.9900, 185 negative triangles 116: dt=0.9900, 156 negative triangles 117: dt=0.9900, 153 negative triangles 118: dt=0.9900, 148 negative triangles 119: dt=0.9900, 152 negative triangles 120: dt=0.9900, 145 negative triangles 121: dt=0.9900, 142 negative triangles 122: dt=0.9900, 142 negative triangles 123: dt=0.9900, 143 negative triangles 124: dt=0.9900, 139 negative triangles 125: dt=0.9900, 138 negative triangles 126: dt=0.9900, 135 negative triangles 127: dt=0.9900, 138 negative triangles 128: dt=0.9900, 134 negative triangles 129: dt=0.9900, 131 negative triangles 130: dt=0.9900, 128 negative triangles 131: dt=0.9900, 130 negative triangles 132: dt=0.9900, 127 negative triangles 133: dt=0.9900, 125 negative triangles 134: dt=0.9900, 125 negative triangles 135: dt=0.9900, 124 negative triangles 136: dt=0.9900, 124 negative triangles 137: dt=0.9900, 121 negative triangles 138: dt=0.9900, 120 negative triangles 139: dt=0.9900, 119 negative triangles 140: dt=0.9900, 118 negative triangles 141: dt=0.9900, 119 negative triangles 142: dt=0.9900, 120 negative triangles 143: dt=0.9900, 119 negative triangles 144: dt=0.9900, 119 negative triangles 145: dt=0.9900, 119 negative triangles 146: dt=0.9900, 119 negative triangles 147: dt=0.9900, 120 negative triangles 148: dt=0.9900, 121 negative triangles 149: dt=0.9900, 120 negative triangles 150: dt=0.9405, 123 negative triangles 151: dt=0.9405, 123 negative triangles 152: dt=0.9405, 119 negative triangles 153: dt=0.9405, 118 negative triangles 154: dt=0.9405, 118 negative triangles 155: dt=0.9405, 119 negative triangles 156: dt=0.9405, 120 negative triangles 157: dt=0.9405, 123 negative triangles 158: dt=0.9405, 125 negative triangles 159: dt=0.9405, 124 negative triangles 160: dt=0.8935, 122 negative triangles 161: dt=0.8935, 119 negative triangles 162: dt=0.8935, 119 negative triangles 163: dt=0.8935, 120 negative triangles 164: dt=0.8935, 119 negative triangles 165: dt=0.8935, 120 negative triangles 166: dt=0.8935, 120 negative triangles 167: dt=0.8935, 119 negative triangles 168: dt=0.8935, 119 negative triangles 169: dt=0.8935, 119 negative triangles 170: dt=0.8488, 120 negative triangles 171: dt=0.8488, 120 negative triangles 172: dt=0.8488, 121 negative triangles 173: dt=0.8488, 122 negative triangles 174: dt=0.8488, 124 negative triangles 175: dt=0.8488, 124 negative triangles 176: dt=0.8488, 123 negative triangles 177: dt=0.8488, 120 negative triangles 178: dt=0.8488, 118 negative triangles 179: dt=0.8488, 119 negative triangles 180: dt=0.8064, 119 negative triangles 181: dt=0.8064, 118 negative triangles 182: dt=0.8064, 117 negative triangles 183: dt=0.8064, 116 negative triangles 184: dt=0.8064, 115 negative triangles 185: dt=0.8064, 118 negative triangles 186: dt=0.8064, 117 negative triangles 187: dt=0.8064, 120 negative triangles 188: dt=0.8064, 116 negative triangles 189: dt=0.8064, 116 negative triangles 190: dt=0.8064, 115 negative triangles 191: dt=0.8064, 115 negative triangles 192: dt=0.8064, 115 negative triangles 193: dt=0.8064, 114 negative triangles 194: dt=0.8064, 115 negative triangles 195: dt=0.8064, 114 negative triangles 196: dt=0.8064, 115 negative triangles 197: dt=0.8064, 115 negative triangles 198: dt=0.8064, 114 negative triangles 199: dt=0.8064, 113 negative triangles 200: dt=0.8064, 113 negative triangles 201: dt=0.8064, 114 negative triangles 202: dt=0.8064, 115 negative triangles 203: dt=0.8064, 116 negative triangles 204: dt=0.8064, 114 negative triangles 205: dt=0.8064, 114 negative triangles 206: dt=0.8064, 113 negative triangles 207: dt=0.8064, 113 negative triangles 208: dt=0.8064, 116 negative triangles 209: dt=0.7660, 116 negative triangles 210: dt=0.7660, 120 negative triangles 211: dt=0.7660, 116 negative triangles 212: dt=0.7660, 116 negative triangles 213: dt=0.7660, 116 negative triangles 214: dt=0.7660, 117 negative triangles 215: dt=0.7660, 117 negative triangles 216: dt=0.7660, 117 negative triangles 217: dt=0.7660, 115 negative triangles 218: dt=0.7660, 116 negative triangles 219: dt=0.7277, 119 negative triangles 220: dt=0.7277, 119 negative triangles 221: dt=0.7277, 118 negative triangles 222: dt=0.7277, 118 negative triangles 223: dt=0.7277, 118 negative triangles 224: dt=0.7277, 117 negative triangles 225: dt=0.7277, 117 negative triangles 226: dt=0.7277, 116 negative triangles 227: dt=0.7277, 117 negative triangles 228: dt=0.7277, 115 negative triangles 229: dt=0.6914, 115 negative triangles 230: dt=0.6914, 116 negative triangles 231: dt=0.6914, 116 negative triangles 232: dt=0.6914, 119 negative triangles 233: dt=0.6914, 118 negative triangles 234: dt=0.6914, 120 negative triangles 235: dt=0.6914, 121 negative triangles 236: dt=0.6914, 120 negative triangles 237: dt=0.6914, 118 negative triangles 238: dt=0.6914, 117 negative triangles 239: dt=0.6568, 117 negative triangles 240: dt=0.6568, 115 negative triangles 241: dt=0.6568, 115 negative triangles 242: dt=0.6568, 116 negative triangles 243: dt=0.6568, 116 negative triangles 244: dt=0.6568, 119 negative triangles 245: dt=0.6568, 118 negative triangles 246: dt=0.6568, 120 negative triangles 247: dt=0.6568, 120 negative triangles 248: dt=0.6568, 119 negative triangles 249: dt=0.6239, 117 negative triangles 250: dt=0.6239, 116 negative triangles 251: dt=0.6239, 116 negative triangles 252: dt=0.6239, 114 negative triangles 253: dt=0.6239, 113 negative triangles 254: dt=0.6239, 114 negative triangles 255: dt=0.6239, 114 negative triangles 256: dt=0.6239, 114 negative triangles 257: dt=0.6239, 116 negative triangles 258: dt=0.6239, 118 negative triangles 259: dt=0.5927, 119 negative triangles 260: dt=0.5927, 119 negative triangles 261: dt=0.5927, 119 negative triangles 262: dt=0.5927, 119 negative triangles 263: dt=0.5927, 117 negative triangles 264: dt=0.5927, 116 negative triangles 265: dt=0.5927, 116 negative triangles 266: dt=0.5927, 115 negative triangles 267: dt=0.5927, 114 negative triangles 268: dt=0.5927, 114 negative triangles 269: dt=0.5631, 116 negative triangles 270: dt=0.5631, 116 negative triangles 271: dt=0.5631, 117 negative triangles 272: dt=0.5631, 119 negative triangles 273: dt=0.5631, 119 negative triangles 274: dt=0.5631, 118 negative triangles 275: dt=0.5631, 117 negative triangles 276: dt=0.5631, 117 negative triangles 277: dt=0.5631, 117 negative triangles 278: dt=0.5631, 116 negative triangles 279: dt=0.5350, 115 negative triangles 280: dt=0.5350, 116 negative triangles 281: dt=0.5350, 116 negative triangles 282: dt=0.5350, 118 negative triangles 283: dt=0.5350, 119 negative triangles 284: dt=0.5350, 118 negative triangles 285: dt=0.5350, 119 negative triangles 286: dt=0.5350, 118 negative triangles 287: dt=0.5350, 117 negative triangles 288: dt=0.5350, 117 negative triangles 289: dt=0.5082, 116 negative triangles 290: dt=0.5082, 115 negative triangles 291: dt=0.5082, 116 negative triangles 292: dt=0.5082, 118 negative triangles 293: dt=0.5082, 118 negative triangles 294: dt=0.5082, 119 negative triangles 295: dt=0.5082, 119 negative triangles 296: dt=0.5082, 120 negative triangles 297: dt=0.5082, 119 negative triangles 298: dt=0.5082, 119 negative triangles 299: dt=0.4828, 117 negative triangles 300: dt=0.4828, 117 negative triangles 301: dt=0.4828, 119 negative triangles 302: dt=0.4828, 117 negative triangles 303: dt=0.4828, 115 negative triangles 304: dt=0.4828, 116 negative triangles 305: dt=0.4828, 118 negative triangles 306: dt=0.4828, 118 negative triangles 307: dt=0.4828, 117 negative triangles 308: dt=0.4828, 116 negative triangles 309: dt=0.4587, 115 negative triangles 310: dt=0.4587, 115 negative triangles 311: dt=0.4587, 116 negative triangles 312: dt=0.4587, 117 negative triangles 313: dt=0.4587, 117 negative triangles 314: dt=0.4587, 117 negative triangles 315: dt=0.4587, 116 negative triangles 316: dt=0.4587, 116 negative triangles 317: dt=0.4587, 115 negative triangles 318: dt=0.4587, 113 negative triangles 319: dt=0.4357, 113 negative triangles 320: dt=0.4357, 113 negative triangles 321: dt=0.4357, 117 negative triangles 322: dt=0.4357, 118 negative triangles 323: dt=0.4357, 118 negative triangles 324: dt=0.4357, 118 negative triangles 325: dt=0.4357, 118 negative triangles 326: dt=0.4357, 119 negative triangles 327: dt=0.4357, 118 negative triangles 328: dt=0.4357, 118 negative triangles 329: dt=0.4139, 118 negative triangles 330: dt=0.4139, 118 negative triangles 331: dt=0.4139, 119 negative triangles 332: dt=0.4139, 119 negative triangles 333: dt=0.4139, 118 negative triangles 334: dt=0.4139, 118 negative triangles 335: dt=0.4139, 119 negative triangles 336: dt=0.4139, 119 negative triangles 337: dt=0.4139, 117 negative triangles 338: dt=0.4139, 117 negative triangles 339: dt=0.3932, 116 negative triangles 340: dt=0.3932, 116 negative triangles 341: dt=0.3932, 116 negative triangles 342: dt=0.3932, 116 negative triangles 343: dt=0.3932, 117 negative triangles 344: dt=0.3932, 113 negative triangles 345: dt=0.3932, 114 negative triangles 346: dt=0.3932, 116 negative triangles 347: dt=0.3932, 117 negative triangles 348: dt=0.3932, 118 negative triangles 349: dt=0.3736, 117 negative triangles 350: dt=0.3736, 119 negative triangles 351: dt=0.3736, 117 negative triangles 352: dt=0.3736, 117 negative triangles 353: dt=0.3736, 116 negative triangles 354: dt=0.3736, 117 negative triangles 355: dt=0.3736, 117 negative triangles 356: dt=0.3736, 116 negative triangles 357: dt=0.3736, 115 negative triangles 358: dt=0.3736, 115 negative triangles 359: dt=0.3549, 114 negative triangles 360: dt=0.3549, 113 negative triangles 361: dt=0.3549, 113 negative triangles 362: dt=0.3549, 114 negative triangles 363: dt=0.3549, 113 negative triangles 364: dt=0.3549, 111 negative triangles 365: dt=0.3549, 111 negative triangles 366: dt=0.3549, 112 negative triangles 367: dt=0.3549, 111 negative triangles 368: dt=0.3549, 111 negative triangles 369: dt=0.3549, 112 negative triangles 370: dt=0.3549, 114 negative triangles 371: dt=0.3549, 117 negative triangles 372: dt=0.3549, 117 negative triangles 373: dt=0.3549, 116 negative triangles 374: dt=0.3372, 115 negative triangles 375: dt=0.3372, 114 negative triangles 376: dt=0.3372, 113 negative triangles 377: dt=0.3372, 112 negative triangles 378: dt=0.3372, 112 negative triangles 379: dt=0.3372, 112 negative triangles 380: dt=0.3372, 112 negative triangles 381: dt=0.3372, 112 negative triangles 382: dt=0.3372, 112 negative triangles 383: dt=0.3372, 112 negative triangles 384: dt=0.3203, 111 negative triangles 385: dt=0.3203, 111 negative triangles 386: dt=0.3203, 112 negative triangles 387: dt=0.3203, 110 negative triangles 388: dt=0.3203, 112 negative triangles 389: dt=0.3203, 112 negative triangles 390: dt=0.3203, 113 negative triangles 391: dt=0.3203, 114 negative triangles 392: dt=0.3203, 114 negative triangles 393: dt=0.3203, 114 negative triangles 394: dt=0.3203, 114 negative triangles 395: dt=0.3203, 113 negative triangles 396: dt=0.3203, 112 negative triangles 397: dt=0.3043, 111 negative triangles 398: dt=0.3043, 111 negative triangles 399: dt=0.3043, 110 negative triangles 400: dt=0.3043, 110 negative triangles 401: dt=0.3043, 110 negative triangles 402: dt=0.3043, 111 negative triangles 403: dt=0.3043, 111 negative triangles 404: dt=0.3043, 111 negative triangles 405: dt=0.3043, 113 negative triangles 406: dt=0.3043, 112 negative triangles 407: dt=0.2891, 113 negative triangles 408: dt=0.2891, 111 negative triangles 409: dt=0.2891, 111 negative triangles 410: dt=0.2891, 112 negative triangles 411: dt=0.2891, 111 negative triangles 412: dt=0.2891, 112 negative triangles 413: dt=0.2891, 111 negative triangles 414: dt=0.2891, 111 negative triangles 415: dt=0.2891, 110 negative triangles 416: dt=0.2891, 110 negative triangles 417: dt=0.2746, 110 negative triangles 418: dt=0.2746, 112 negative triangles 419: dt=0.2746, 112 negative triangles 420: dt=0.2746, 112 negative triangles 421: dt=0.2746, 113 negative triangles 422: dt=0.2746, 113 negative triangles 423: dt=0.2746, 114 negative triangles 424: dt=0.2746, 114 negative triangles 425: dt=0.2746, 113 negative triangles 426: dt=0.2746, 113 negative triangles 427: dt=0.2609, 113 negative triangles 428: dt=0.2609, 113 negative triangles 429: dt=0.2609, 112 negative triangles 430: dt=0.2609, 111 negative triangles 431: dt=0.2609, 111 negative triangles 432: dt=0.2609, 112 negative triangles 433: dt=0.2609, 114 negative triangles 434: dt=0.2609, 113 negative triangles 435: dt=0.2609, 111 negative triangles 436: dt=0.2609, 111 negative triangles 437: dt=0.2478, 111 negative triangles 438: dt=0.2478, 112 negative triangles 439: dt=0.2478, 111 negative triangles 440: dt=0.2478, 111 negative triangles 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negative triangles 467: dt=0.2125, 113 negative triangles 468: dt=0.2125, 112 negative triangles 469: dt=0.2125, 112 negative triangles 470: dt=0.2125, 111 negative triangles 471: dt=0.2125, 112 negative triangles 472: dt=0.2125, 113 negative triangles 473: dt=0.2125, 113 negative triangles 474: dt=0.2125, 112 negative triangles 475: dt=0.2125, 113 negative triangles 476: dt=0.2125, 114 negative triangles 477: dt=0.2019, 113 negative triangles 478: dt=0.2019, 114 negative triangles 479: dt=0.2019, 114 negative triangles 480: dt=0.2019, 113 negative triangles 481: dt=0.2019, 115 negative triangles 482: dt=0.2019, 115 negative triangles 483: dt=0.2019, 114 negative triangles 484: dt=0.2019, 114 negative triangles 485: dt=0.2019, 115 negative triangles 486: dt=0.2019, 114 negative triangles 487: dt=0.1918, 114 negative triangles 488: dt=0.1918, 114 negative triangles 489: dt=0.1918, 114 negative triangles 490: dt=0.1918, 115 negative triangles 491: dt=0.1918, 114 negative triangles 492: 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111 negative triangles 544: dt=0.1484, 110 negative triangles 545: dt=0.1484, 110 negative triangles 546: dt=0.1484, 111 negative triangles 547: dt=0.1484, 109 negative triangles 548: dt=0.1410, 109 negative triangles 549: dt=0.1410, 109 negative triangles 550: dt=0.1410, 109 negative triangles 551: dt=0.1410, 110 negative triangles 552: dt=0.1410, 110 negative triangles 553: dt=0.1410, 109 negative triangles 554: dt=0.1410, 109 negative triangles 555: dt=0.1410, 110 negative triangles 556: dt=0.1410, 110 negative triangles 557: dt=0.1410, 110 negative triangles 558: dt=0.1339, 111 negative triangles 559: dt=0.1339, 112 negative triangles 560: dt=0.1339, 112 negative triangles 561: dt=0.1339, 111 negative triangles 562: dt=0.1339, 112 negative triangles 563: dt=0.1339, 112 negative triangles 564: dt=0.1339, 113 negative triangles 565: dt=0.1339, 112 negative triangles 566: dt=0.1339, 112 negative triangles 567: dt=0.1339, 112 negative triangles 568: dt=0.1272, 112 negative triangles 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negative triangles 595: dt=0.1148, 109 negative triangles 596: dt=0.1148, 111 negative triangles 597: dt=0.1148, 111 negative triangles 598: dt=0.1091, 111 negative triangles 599: dt=0.1091, 111 negative triangles 600: dt=0.1091, 110 negative triangles 601: dt=0.1091, 111 negative triangles 602: dt=0.1091, 110 negative triangles 603: dt=0.1091, 110 negative triangles 604: dt=0.1091, 110 negative triangles 605: dt=0.1091, 111 negative triangles 606: dt=0.1091, 111 negative triangles 607: dt=0.1091, 111 negative triangles 608: dt=0.1036, 110 negative triangles 609: dt=0.1036, 110 negative triangles 610: dt=0.1036, 110 negative triangles 611: dt=0.1036, 111 negative triangles 612: dt=0.1036, 110 negative triangles 613: dt=0.1036, 110 negative triangles 614: dt=0.1036, 111 negative triangles 615: dt=0.1036, 111 negative triangles 616: dt=0.1036, 111 negative triangles 617: dt=0.1036, 112 negative triangles 618: dt=0.0984, 111 negative triangles 619: dt=0.0984, 111 negative triangles 620: 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107 negative triangles 672: dt=0.0844, 108 negative triangles 673: dt=0.0844, 108 negative triangles 674: dt=0.0844, 107 negative triangles 675: dt=0.0844, 107 negative triangles 676: dt=0.0802, 107 negative triangles 677: dt=0.0802, 108 negative triangles 678: dt=0.0802, 107 negative triangles 679: dt=0.0802, 107 negative triangles 680: dt=0.0802, 107 negative triangles 681: dt=0.0802, 109 negative triangles 682: dt=0.0802, 108 negative triangles 683: dt=0.0802, 107 negative triangles 684: dt=0.0802, 107 negative triangles 685: dt=0.0802, 107 negative triangles 686: dt=0.0762, 108 negative triangles 687: dt=0.0762, 107 negative triangles 688: dt=0.0762, 106 negative triangles 689: dt=0.0762, 106 negative triangles 690: dt=0.0762, 107 negative triangles 691: dt=0.0762, 107 negative triangles 692: dt=0.0762, 106 negative triangles 693: dt=0.0762, 106 negative triangles 694: dt=0.0762, 106 negative triangles 695: dt=0.0762, 107 negative triangles 696: dt=0.0724, 108 negative triangles 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negative triangles 723: dt=0.0653, 108 negative triangles 724: dt=0.0653, 108 negative triangles 725: dt=0.0653, 108 negative triangles 726: dt=0.0620, 109 negative triangles 727: dt=0.0620, 110 negative triangles 728: dt=0.0620, 109 negative triangles 729: dt=0.0620, 109 negative triangles 730: dt=0.0620, 110 negative triangles 731: dt=0.0620, 110 negative triangles 732: dt=0.0620, 109 negative triangles 733: dt=0.0620, 110 negative triangles 734: dt=0.0620, 110 negative triangles 735: dt=0.0620, 111 negative triangles 736: dt=0.0589, 110 negative triangles 737: dt=0.0589, 109 negative triangles 738: dt=0.0589, 111 negative triangles 739: dt=0.0589, 109 negative triangles 740: dt=0.0589, 110 negative triangles 741: dt=0.0589, 109 negative triangles 742: dt=0.0589, 109 negative triangles 743: dt=0.0589, 109 negative triangles 744: dt=0.0589, 110 negative triangles 745: dt=0.0589, 111 negative triangles 746: dt=0.0560, 109 negative triangles 747: dt=0.0560, 109 negative triangles 748: 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105 negative triangles 800: dt=0.0480, 106 negative triangles 801: dt=0.0456, 105 negative triangles 802: dt=0.0456, 105 negative triangles 803: dt=0.0456, 105 negative triangles 804: dt=0.0456, 107 negative triangles 805: dt=0.0456, 106 negative triangles 806: dt=0.0456, 105 negative triangles 807: dt=0.0456, 105 negative triangles 808: dt=0.0456, 106 negative triangles 809: dt=0.0456, 105 negative triangles 810: dt=0.0456, 105 negative triangles 811: dt=0.0433, 105 negative triangles 812: dt=0.0433, 105 negative triangles 813: dt=0.0433, 106 negative triangles 814: dt=0.0433, 106 negative triangles 815: dt=0.0433, 104 negative triangles 816: dt=0.0433, 104 negative triangles 817: dt=0.0433, 105 negative triangles 818: dt=0.0433, 104 negative triangles 819: dt=0.0433, 104 negative triangles 820: dt=0.0433, 104 negative triangles 821: dt=0.0412, 104 negative triangles 822: dt=0.0412, 106 negative triangles 823: dt=0.0412, 106 negative triangles 824: dt=0.0412, 105 negative triangles 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negative triangles 851: dt=0.0353, 106 negative triangles 852: dt=0.0353, 106 negative triangles 853: dt=0.0353, 107 negative triangles 854: dt=0.0353, 107 negative triangles 855: dt=0.0353, 106 negative triangles 856: dt=0.0353, 106 negative triangles 857: dt=0.0353, 106 negative triangles 858: dt=0.0353, 107 negative triangles 859: dt=0.0353, 106 negative triangles 860: dt=0.0353, 106 negative triangles 861: dt=0.0335, 106 negative triangles 862: dt=0.0335, 107 negative triangles 863: dt=0.0335, 106 negative triangles 864: dt=0.0335, 105 negative triangles 865: dt=0.0335, 105 negative triangles 866: dt=0.0335, 105 negative triangles 867: dt=0.0335, 106 negative triangles 868: dt=0.0335, 105 negative triangles 869: dt=0.0335, 105 negative triangles 870: dt=0.0335, 105 negative triangles 871: dt=0.0319, 107 negative triangles 872: dt=0.0319, 106 negative triangles 873: dt=0.0319, 105 negative triangles 874: dt=0.0319, 105 negative triangles 875: dt=0.0319, 105 negative triangles 876: dt=0.0319, 106 negative triangles 877: dt=0.0319, 107 negative triangles 878: dt=0.0319, 105 negative triangles 879: dt=0.0319, 105 negative triangles 880: dt=0.0319, 105 negative triangles 881: dt=0.0303, 106 negative triangles 882: dt=0.0303, 105 negative triangles 883: dt=0.0303, 105 negative triangles 884: dt=0.0303, 106 negative triangles 885: dt=0.0303, 105 negative triangles 886: dt=0.0303, 106 negative triangles 887: dt=0.0303, 106 negative triangles 888: dt=0.0303, 104 negative triangles 889: dt=0.0303, 104 negative triangles 890: dt=0.0303, 105 negative triangles 891: dt=0.0287, 104 negative triangles 892: dt=0.0287, 104 negative triangles 893: dt=0.0287, 104 negative triangles 894: dt=0.0287, 104 negative triangles 895: dt=0.0287, 105 negative triangles 896: dt=0.0287, 106 negative triangles 897: dt=0.0287, 105 negative triangles 898: dt=0.0287, 104 negative triangles 899: dt=0.0287, 105 negative triangles 900: dt=0.0287, 104 negative triangles 901: dt=0.0273, 104 negative 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105 negative triangles 928: dt=0.0246, 105 negative triangles 929: dt=0.0246, 105 negative triangles 930: dt=0.0246, 106 negative triangles 931: dt=0.0234, 107 negative triangles 932: dt=0.0234, 105 negative triangles 933: dt=0.0234, 105 negative triangles 934: dt=0.0234, 106 negative triangles 935: dt=0.0234, 105 negative triangles 936: dt=0.0234, 105 negative triangles 937: dt=0.0234, 105 negative triangles 938: dt=0.0234, 106 negative triangles 939: dt=0.0234, 106 negative triangles 940: dt=0.0234, 106 negative triangles 941: dt=0.0222, 105 negative triangles 942: dt=0.0222, 105 negative triangles 943: dt=0.0222, 106 negative triangles 944: dt=0.0222, 105 negative triangles 945: dt=0.0222, 105 negative triangles 946: dt=0.0222, 105 negative triangles 947: dt=0.0222, 105 negative triangles 948: dt=0.0222, 106 negative triangles 949: dt=0.0222, 106 negative triangles 950: dt=0.0222, 105 negative triangles 951: dt=0.0211, 105 negative triangles 952: dt=0.0211, 106 negative triangles 953: dt=0.0211, 105 negative triangles 954: dt=0.0211, 105 negative triangles 955: dt=0.0211, 105 negative triangles 956: dt=0.0211, 105 negative triangles 957: dt=0.0211, 106 negative triangles 958: dt=0.0211, 106 negative triangles 959: dt=0.0211, 104 negative triangles 960: dt=0.0211, 104 negative triangles 961: dt=0.0201, 104 negative triangles 962: dt=0.0201, 104 negative triangles 963: dt=0.0201, 104 negative triangles 964: dt=0.0201, 104 negative triangles 965: dt=0.0201, 105 negative triangles 966: dt=0.0201, 105 negative triangles 967: dt=0.0201, 104 negative triangles 968: dt=0.0201, 104 negative triangles 969: dt=0.0201, 104 negative triangles 970: dt=0.0201, 104 negative triangles 971: dt=0.0191, 105 negative triangles 972: dt=0.0191, 107 negative triangles 973: dt=0.0191, 105 negative triangles 974: dt=0.0191, 105 negative triangles 975: dt=0.0191, 105 negative triangles 976: dt=0.0191, 106 negative triangles 977: dt=0.0191, 105 negative triangles 978: dt=0.0191, 106 negative triangles 979: dt=0.0191, 104 negative triangles 980: dt=0.0191, 104 negative triangles 981: dt=0.0181, 105 negative triangles 982: dt=0.0181, 104 negative triangles 983: dt=0.0181, 105 negative triangles 984: dt=0.0181, 105 negative triangles 985: dt=0.0181, 105 negative triangles 986: dt=0.0181, 107 negative triangles 987: dt=0.0181, 106 negative triangles 988: dt=0.0181, 105 negative triangles 989: dt=0.0181, 105 negative triangles 990: dt=0.0181, 106 negative triangles 991: dt=0.0172, 105 negative triangles 992: dt=0.0172, 105 negative triangles 993: dt=0.0172, 105 negative triangles 994: dt=0.0172, 104 negative triangles 995: dt=0.0172, 106 negative triangles 996: dt=0.0172, 105 negative triangles 997: dt=0.0172, 105 negative triangles 998: dt=0.0172, 104 negative triangles 999: dt=0.0172, 105 negative triangles 1000: dt=0.0172, 105 negative triangles 1001: dt=0.0164, 105 negative triangles 1002: dt=0.0164, 104 negative triangles 1003: dt=0.0164, 105 negative triangles 1004: dt=0.0164, 106 negative triangles 1005: dt=0.0164, 105 negative triangles 1006: dt=0.0164, 104 negative triangles 1007: dt=0.0164, 104 negative triangles 1008: dt=0.0164, 104 negative triangles 1009: dt=0.0164, 106 negative triangles 1010: dt=0.0164, 105 negative triangles 1011: dt=0.0155, 104 negative triangles 1012: dt=0.0155, 104 negative triangles 1013: dt=0.0155, 104 negative triangles 1014: dt=0.0155, 105 negative triangles 1015: dt=0.0155, 107 negative triangles 1016: dt=0.0155, 105 negative triangles 1017: dt=0.0155, 104 negative triangles 1018: dt=0.0155, 104 negative triangles 1019: dt=0.0155, 105 negative triangles 1020: dt=0.0155, 104 negative triangles 1021: dt=0.0148, 104 negative triangles 1022: dt=0.0148, 104 negative triangles 1023: dt=0.0148, 106 negative triangles 1024: dt=0.0148, 105 negative triangles 1025: dt=0.0148, 104 negative triangles 1026: dt=0.0148, 104 negative triangles 1027: dt=0.0148, 105 negative triangles 1028: dt=0.0148, 104 negative triangles 1029: dt=0.0148, 104 negative triangles 1030: dt=0.0148, 104 negative triangles 1031: dt=0.0140, 105 negative triangles 1032: dt=0.0140, 105 negative triangles 1033: dt=0.0140, 104 negative triangles 1034: dt=0.0140, 104 negative triangles 1035: dt=0.0140, 105 negative triangles 1036: dt=0.0140, 104 negative triangles 1037: dt=0.0140, 104 negative triangles 1038: dt=0.0140, 104 negative triangles 1039: dt=0.0140, 104 negative triangles 1040: dt=0.0140, 105 negative triangles 1041: dt=0.0133, 105 negative triangles 1042: dt=0.0133, 104 negative triangles 1043: dt=0.0133, 104 negative triangles 1044: dt=0.0133, 105 negative triangles 1045: dt=0.0133, 104 negative triangles 1046: dt=0.0133, 104 negative triangles 1047: dt=0.0133, 104 negative triangles 1048: dt=0.0133, 105 negative triangles 1049: dt=0.0133, 105 negative triangles 1050: dt=0.0133, 104 negative triangles 1051: dt=0.0127, 104 negative triangles 1052: dt=0.0127, 105 negative triangles 1053: dt=0.0127, 104 negative triangles 1054: dt=0.0127, 105 negative triangles 1055: dt=0.0127, 105 negative triangles 1056: dt=0.0127, 105 negative triangles 1057: dt=0.0127, 106 negative triangles 1058: dt=0.0127, 106 negative triangles 1059: dt=0.0127, 105 negative triangles 1060: dt=0.0127, 105 negative triangles 1061: dt=0.0120, 106 negative triangles 1062: dt=0.0120, 105 negative triangles 1063: dt=0.0120, 105 negative triangles 1064: dt=0.0120, 105 negative triangles 1065: dt=0.0120, 106 negative triangles 1066: dt=0.0120, 106 negative triangles 1067: dt=0.0120, 105 negative triangles 1068: dt=0.0120, 106 negative triangles 1069: dt=0.0120, 105 negative triangles 1070: dt=0.0120, 105 negative triangles 1071: dt=0.0114, 106 negative triangles 1072: dt=0.0114, 107 negative triangles 1073: dt=0.0114, 107 negative triangles 1074: dt=0.0114, 106 negative triangles 1075: dt=0.0114, 107 negative triangles 1076: dt=0.0114, 106 negative triangles 1077: dt=0.0114, 106 negative triangles 1078: dt=0.0114, 106 negative triangles 1079: dt=0.0114, 107 negative triangles 1080: dt=0.0114, 106 negative triangles 1081: dt=0.0108, 108 negative triangles 1082: dt=0.0108, 106 negative triangles 1083: dt=0.0108, 107 negative triangles 1084: dt=0.0108, 106 negative triangles 1085: dt=0.0108, 105 negative triangles 1086: dt=0.0108, 107 negative triangles 1087: dt=0.0108, 107 negative triangles 1088: dt=0.0108, 106 negative triangles 1089: dt=0.0108, 105 negative triangles 1090: dt=0.0108, 107 negative triangles 1091: dt=0.0103, 106 negative triangles 1092: dt=0.0103, 106 negative triangles 1093: dt=0.0103, 107 negative triangles 1094: dt=0.0103, 108 negative triangles 1095: dt=0.0103, 106 negative triangles 1096: dt=0.0103, 106 negative triangles 1097: dt=0.0103, 106 negative triangles 1098: dt=0.0103, 108 negative triangles 1099: dt=0.0103, 108 negative triangles 1100: dt=0.0103, 107 negative triangles 1101: dt=0.0098, 106 negative triangles 1102: dt=0.0098, 107 negative triangles 1103: dt=0.0098, 106 negative triangles 1104: dt=0.0098, 107 negative triangles 1105: dt=0.0098, 107 negative triangles 1106: dt=0.0098, 107 negative triangles 1107: dt=0.0098, 107 negative triangles 1108: dt=0.0098, 106 negative triangles 1109: dt=0.0098, 107 negative triangles 1110: dt=0.0098, 107 negative triangles 1111: dt=0.0098, 107 negative triangles 1112: dt=0.0098, 105 negative triangles 1113: dt=0.0098, 107 negative triangles writing registered surface to ../surf/rh.sphere.reg... 1114: dt=0.0098, 107 negative triangles 1115: 105 negative triangles registration took 0.93 hours FSRUNTIME@ mris_register 0.9302 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Wed Jan 27 22:02:55 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white \n reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Wed Jan 27 22:02:59 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white \n reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Wed Jan 27 22:03:02 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mrisp_paint -a 5 /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv \n 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... #-------------------------------------------- #@# AvgCurv rh Wed Jan 27 22:03:05 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mrisp_paint -a 5 /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv \n 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 lh Wed Jan 27 22:03:08 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert.Darwin lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot \n setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 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... 1442 labels changed using aseg relabeling using gibbs priors... 000: 2950 changed, 133016 examined... 001: 678 changed, 12753 examined... 002: 163 changed, 3765 examined... 003: 60 changed, 911 examined... 004: 28 changed, 346 examined... 005: 11 changed, 142 examined... 006: 7 changed, 69 examined... 007: 5 changed, 43 examined... 008: 1 changed, 23 examined... 009: 0 changed, 5 examined... 147 labels changed using aseg 000: 111 total segments, 69 labels (195 vertices) changed 001: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1628 vertices marked for relabeling... 1628 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Cortical Parc rh Wed Jan 27 22:03:31 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert.Darwin rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 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... 1244 labels changed using aseg relabeling using gibbs priors... 000: 2803 changed, 131968 examined... 001: 699 changed, 11926 examined... 002: 173 changed, 3849 examined... 003: 69 changed, 1046 examined... 004: 18 changed, 369 examined... 005: 8 changed, 105 examined... 006: 3 changed, 53 examined... 007: 3 changed, 17 examined... 008: 2 changed, 17 examined... 009: 2 changed, 16 examined... 010: 0 changed, 7 examined... 172 labels changed using aseg 000: 95 total segments, 55 labels (379 vertices) changed 001: 41 total segments, 1 labels (2 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 995 vertices marked for relabeling... 995 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 21 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Jan 27 22:03:52 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs bert.Darwin lh \n reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/filled.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/brain.finalsurfs.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/../mri/aseg.presurf.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... 18558 bright wm thresholded. 10474 bright non-wm voxels segmented. reading original surface position from /space/freesurfer/subjects/test/bert.Darwin/surf/lh.orig... computing class statistics... border white: 259765 voxels (1.55%) border gray 279898 voxels (1.67%) WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.2 +- 9.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 62.8 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 53.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-2.6, GM=82+-6.1 mean inside = 100.4, mean outside = 88.0 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group reading initial pial vertex positions from white... mean border=69.8, 66 (66) missing vertices, mean dist 1.9 [0.3 (%0.0)->2.9 (%100.0))] %18 local maxima, %44 large gradients and %33 min vals, 328 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=gust., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=16936118.0, rms=25.441 001: dt: 0.0500, sse=15371639.0, rms=24.190 (4.918%) 002: dt: 0.0500, sse=14297671.0, rms=23.292 (3.713%) 003: dt: 0.0500, sse=13471591.0, rms=22.576 (3.071%) 004: dt: 0.0500, sse=12794134.0, rms=21.972 (2.675%) 005: dt: 0.0500, sse=12214634.0, rms=21.442 (2.413%) 006: dt: 0.0500, sse=11705399.0, rms=20.965 (2.225%) 007: dt: 0.0500, sse=11248629.0, rms=20.528 (2.087%) 008: dt: 0.0500, sse=10832704.0, rms=20.121 (1.981%) 009: dt: 0.0500, sse=10449382.0, rms=19.739 (1.900%) 010: dt: 0.0500, sse=10093170.0, rms=19.377 (1.834%) positioning took 1.2 minutes mean border=69.6, 51 (35) missing vertices, mean dist 1.6 [0.2 (%0.0)->2.4 (%100.0))] %18 local maxima, %44 large gradients and %32 min vals, 301 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=10759499.0, rms=20.050 011: dt: 0.0500, sse=10424582.0, rms=19.715 (1.670%) 012: dt: 0.0500, sse=10110180.0, rms=19.395 (1.621%) 013: dt: 0.0500, sse=9813806.0, rms=19.089 (1.579%) 014: dt: 0.0500, sse=9533865.0, rms=18.795 (1.540%) 015: dt: 0.0500, sse=9268616.0, rms=18.512 (1.505%) 016: dt: 0.0500, sse=9017055.0, rms=18.240 (1.472%) 017: dt: 0.0500, sse=8778242.0, rms=17.977 (1.440%) 018: dt: 0.0500, sse=8551327.0, rms=17.724 (1.408%) 019: dt: 0.0500, sse=8335442.0, rms=17.480 (1.379%) 020: dt: 0.0500, sse=8129812.5, rms=17.244 (1.350%) positioning took 1.2 minutes mean border=69.5, 53 (25) missing vertices, mean dist 1.3 [0.1 (%0.3)->2.0 (%99.7))] %19 local maxima, %44 large gradients and %32 min vals, 302 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8216489.0, rms=17.348 021: dt: 0.0500, sse=8017064.0, rms=17.117 (1.330%) 022: dt: 0.0500, sse=7827048.5, rms=16.895 (1.302%) 023: dt: 0.0500, sse=7645224.5, rms=16.679 (1.279%) 024: dt: 0.0500, sse=7471527.0, rms=16.469 (1.254%) 025: dt: 0.0500, sse=7305585.0, rms=16.267 (1.229%) 026: dt: 0.0500, sse=7146795.5, rms=16.071 (1.206%) 027: dt: 0.0500, sse=6994230.0, rms=15.880 (1.188%) 028: dt: 0.0500, sse=6846888.5, rms=15.693 (1.175%) 029: dt: 0.0500, sse=6704244.0, rms=15.510 (1.165%) 030: dt: 0.0500, sse=6566108.5, rms=15.331 (1.156%) positioning took 1.2 minutes mean border=69.4, 73 (21) missing vertices, mean dist 1.1 [0.1 (%4.3)->1.8 (%95.7))] %19 local maxima, %44 large gradients and %31 min vals, 303 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., 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=6641027.0, rms=15.428 031: dt: 0.5000, sse=5636110.5, rms=14.064 (8.841%) 032: dt: 0.5000, sse=4821918.0, rms=12.848 (8.644%) 033: dt: 0.5000, sse=4090940.5, rms=11.652 (9.313%) 034: dt: 0.5000, sse=3403674.2, rms=10.399 (10.755%) 035: dt: 0.5000, sse=2785857.2, rms=9.129 (12.211%) 036: dt: 0.5000, sse=2254088.8, rms=7.870 (13.785%) 037: dt: 0.5000, sse=1829880.1, rms=6.705 (14.805%) 038: dt: 0.5000, sse=1535395.8, rms=5.752 (14.222%) 039: dt: 0.5000, sse=1349783.9, rms=5.068 (11.891%) 040: dt: 0.5000, sse=1242097.2, rms=4.615 (8.942%) 041: dt: 0.5000, sse=1178940.1, rms=4.336 (6.040%) 042: dt: 0.5000, sse=1144197.1, rms=4.166 (3.921%) 043: dt: 0.5000, sse=1121682.5, rms=4.062 (2.499%) 044: dt: 0.5000, sse=1109823.0, rms=3.996 (1.609%) rms = 3.95, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1100096.2, rms=3.954 (1.060%) 046: dt: 0.2500, sse=997513.8, rms=3.317 (16.109%) 047: dt: 0.2500, sse=970544.5, rms=3.148 (5.106%) rms = 3.14, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=969990.4, rms=3.138 (0.315%) 049: dt: 0.1250, sse=956998.9, rms=3.047 (2.892%) rms = 3.03, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=955071.2, rms=3.034 (0.440%) positioning took 2.7 minutes mean border=68.2, 1615 (8) missing vertices, mean dist 0.1 [0.2 (%43.8)->0.4 (%56.2))] %36 local maxima, %30 large gradients and %27 min vals, 194 gradients ignored tol=1.0e-04, sigma=1.0, host=gust., 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=1233421.2, rms=3.749 051: dt: 0.5000, sse=1165462.2, rms=3.380 (9.841%) 052: dt: 0.5000, sse=1145852.0, rms=3.294 (2.550%) rms = 3.41, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1051613.5, rms=2.596 (21.169%) 054: dt: 0.2500, sse=1022380.8, rms=2.333 (10.127%) 055: dt: 0.2500, sse=1016798.9, rms=2.281 (2.257%) rms = 2.25, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1012730.7, rms=2.246 (1.529%) 057: dt: 0.1250, sse=998847.9, rms=2.107 (6.203%) rms = 2.08, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=996317.1, rms=2.084 (1.097%) positioning took 1.2 minutes mean border=67.4, 1852 (3) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))] %49 local maxima, %19 large gradients and %25 min vals, 174 gradients ignored tol=1.0e-04, sigma=0.5, host=gust., 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=1034619.8, rms=2.480 rms = 2.70, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1007425.4, rms=2.242 (9.614%) 060: dt: 0.2500, sse=996451.6, rms=2.143 (4.393%) rms = 2.12, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=993211.5, rms=2.120 (1.098%) 062: dt: 0.1250, sse=986576.8, rms=2.048 (3.369%) rms = 2.03, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=984470.1, rms=2.030 (0.873%) positioning took 0.8 minutes mean border=66.9, 3374 (3) missing vertices, mean dist 0.0 [0.2 (%46.1)->0.2 (%53.9))] %52 local maxima, %15 large gradients and %25 min vals, 167 gradients ignored tol=1.0e-04, sigma=0.2, host=gust., 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 /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=995032.4, rms=2.143 rms = 2.38, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=984015.4, rms=2.032 (5.175%) rms = 1.99, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=978963.1, rms=1.991 (2.024%) rms = 1.94, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=974736.8, rms=1.942 (2.437%) positioning took 0.5 minutes writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/lh.area.pial vertex spacing 1.00 +- 0.44 (0.09-->7.46) (max @ vno 84333 --> 83425) face area 0.39 +- 0.31 (0.00-->6.47) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133016 vertices processed 25000 of 133016 vertices processed 50000 of 133016 vertices processed 75000 of 133016 vertices processed 100000 of 133016 vertices processed 125000 of 133016 vertices processed 0 of 133016 vertices processed 25000 of 133016 vertices processed 50000 of 133016 vertices processed 75000 of 133016 vertices processed 100000 of 133016 vertices processed 125000 of 133016 vertices processed thickness calculation complete, 325:746 truncations. 29766 vertices at 0 distance 90640 vertices at 1 distance 79010 vertices at 2 distance 34386 vertices at 3 distance 11895 vertices at 4 distance 3958 vertices at 5 distance 1360 vertices at 6 distance 512 vertices at 7 distance 185 vertices at 8 distance 88 vertices at 9 distance 44 vertices at 10 distance 41 vertices at 11 distance 39 vertices at 12 distance 19 vertices at 13 distance 8 vertices at 14 distance 12 vertices at 15 distance 7 vertices at 16 distance 3 vertices at 17 distance 2 vertices at 18 distance 6 vertices at 19 distance 5 vertices at 20 distance writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/lh.thickness positioning took 11.3 minutes #-------------------------------------------- #@# Make Pial Surf rh Wed Jan 27 22:15:08 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs bert.Darwin rh \n reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/filled.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/brain.finalsurfs.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/../mri/aseg.presurf.mgz... reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... 18558 bright wm thresholded. 10474 bright non-wm voxels segmented. reading original surface position from /space/freesurfer/subjects/test/bert.Darwin/surf/rh.orig... computing class statistics... border white: 259765 voxels (1.55%) border gray 279898 voxels (1.67%) WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.2 +- 9.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 63.8 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 54.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-3.5, GM=83+-6.1 mean inside = 100.5, mean outside = 88.4 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=70.8, 47 (47) missing vertices, mean dist 1.9 [3.9 (%0.0)->2.9 (%100.0))] %18 local maxima, %45 large gradients and %31 min vals, 358 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=gust., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=16045547.0, rms=24.775 001: dt: 0.0500, sse=14561371.0, rms=23.552 (4.936%) 002: dt: 0.0500, sse=13545169.0, rms=22.677 (3.718%) 003: dt: 0.0500, sse=12763978.0, rms=21.980 (3.073%) 004: dt: 0.0500, sse=12124255.0, rms=21.392 (2.674%) 005: dt: 0.0500, sse=11578005.0, rms=20.877 (2.408%) 006: dt: 0.0500, sse=11099087.0, rms=20.415 (2.215%) 007: dt: 0.0500, sse=10669709.0, rms=19.991 (2.075%) 008: dt: 0.0500, sse=10279241.0, rms=19.598 (1.967%) 009: dt: 0.0500, sse=9919968.0, rms=19.229 (1.883%) 010: dt: 0.0500, sse=9586687.0, rms=18.880 (1.814%) positioning took 1.2 minutes mean border=70.6, 42 (24) missing vertices, mean dist 1.6 [2.3 (%0.0)->2.3 (%100.0))] %19 local maxima, %45 large gradients and %30 min vals, 368 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=10208050.0, rms=19.527 011: dt: 0.0500, sse=9895136.0, rms=19.204 (1.651%) 012: dt: 0.0500, sse=9601620.0, rms=18.897 (1.601%) 013: dt: 0.0500, sse=9325516.0, rms=18.603 (1.555%) 014: dt: 0.0500, sse=9064842.0, rms=18.321 (1.515%) 015: dt: 0.0500, sse=8818354.0, rms=18.051 (1.477%) 016: dt: 0.0500, sse=8584947.0, rms=17.790 (1.441%) 017: dt: 0.0500, sse=8363700.0, rms=17.540 (1.407%) 018: dt: 0.0500, sse=8153820.5, rms=17.299 (1.373%) 019: dt: 0.0500, sse=7954405.5, rms=17.067 (1.341%) 020: dt: 0.0500, sse=7764511.0, rms=16.843 (1.313%) positioning took 1.2 minutes mean border=70.4, 53 (22) missing vertices, mean dist 1.4 [0.1 (%0.3)->2.0 (%99.7))] %20 local maxima, %45 large gradients and %30 min vals, 333 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=7873174.5, rms=16.977 021: dt: 0.0500, sse=7688729.0, rms=16.758 (1.289%) 022: dt: 0.0500, sse=7512925.0, rms=16.547 (1.261%) 023: dt: 0.0500, sse=7344672.5, rms=16.342 (1.238%) 024: dt: 0.0500, sse=7183989.5, rms=16.144 (1.213%) 025: dt: 0.0500, sse=7030340.0, rms=15.952 (1.189%) 026: dt: 0.0500, sse=6882817.0, rms=15.765 (1.169%) 027: dt: 0.0500, sse=6740664.5, rms=15.583 (1.154%) 028: dt: 0.0500, sse=6602809.0, rms=15.405 (1.146%) 029: dt: 0.0500, sse=6469002.0, rms=15.229 (1.139%) 030: dt: 0.0500, sse=6338878.0, rms=15.057 (1.134%) positioning took 1.2 minutes mean border=70.3, 83 (20) missing vertices, mean dist 1.1 [0.1 (%4.1)->1.7 (%95.9))] %20 local maxima, %46 large gradients and %29 min vals, 334 gradients ignored tol=1.0e-04, sigma=2.0, host=gust., 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=6399542.0, rms=15.137 031: dt: 0.5000, sse=5445006.5, rms=13.812 (8.753%) 032: dt: 0.5000, sse=4660445.0, rms=12.615 (8.671%) 033: dt: 0.5000, sse=3939494.0, rms=11.407 (9.573%) 034: dt: 0.5000, sse=3269771.5, rms=10.154 (10.986%) 035: dt: 0.5000, sse=2663893.5, rms=8.873 (12.619%) 036: dt: 0.5000, sse=2136028.5, rms=7.579 (14.583%) 037: dt: 0.5000, sse=1719543.6, rms=6.380 (15.815%) 038: dt: 0.5000, sse=1444200.9, rms=5.439 (14.751%) 039: dt: 0.5000, sse=1270965.2, rms=4.760 (12.491%) 040: dt: 0.5000, sse=1185999.0, rms=4.380 (7.974%) 041: dt: 0.5000, sse=1130560.9, rms=4.123 (5.880%) 042: dt: 0.5000, sse=1109468.8, rms=4.013 (2.666%) 043: dt: 0.5000, sse=1087864.9, rms=3.909 (2.579%) rms = 3.89, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=1084492.4, rms=3.886 (0.588%) 045: dt: 0.2500, sse=980401.6, rms=3.233 (16.798%) 046: dt: 0.2500, sse=955261.7, rms=3.068 (5.126%) rms = 3.05, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=953621.4, rms=3.053 (0.483%) 048: dt: 0.1250, sse=941117.8, rms=2.963 (2.951%) rms = 2.95, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=939339.1, rms=2.950 (0.419%) positioning took 2.5 minutes mean border=69.1, 1539 (3) missing vertices, mean dist 0.1 [0.2 (%41.4)->0.4 (%58.6))] %39 local maxima, %29 large gradients and %25 min vals, 135 gradients ignored tol=1.0e-04, sigma=1.0, host=gust., 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=1224344.8, rms=3.753 050: dt: 0.5000, sse=1142036.2, rms=3.293 (12.278%) 051: dt: 0.5000, sse=1118854.6, rms=3.180 (3.424%) rms = 3.32, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=1028026.2, rms=2.479 (22.024%) 053: dt: 0.2500, sse=999336.4, rms=2.207 (10.993%) 054: dt: 0.2500, sse=993236.2, rms=2.146 (2.762%) rms = 2.11, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=989548.6, rms=2.113 (1.528%) 056: dt: 0.1250, sse=976720.9, rms=1.975 (6.527%) rms = 1.95, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=974343.9, rms=1.952 (1.196%) positioning took 1.2 minutes mean border=68.2, 1756 (2) missing vertices, mean dist 0.1 [0.2 (%42.3)->0.3 (%57.7))] %52 local maxima, %18 large gradients and %24 min vals, 139 gradients ignored tol=1.0e-04, sigma=0.5, host=gust., 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=1018122.6, rms=2.418 rms = 2.61, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=984872.6, rms=2.114 (12.560%) 059: dt: 0.2500, sse=970402.8, rms=1.969 (6.861%) rms = 1.93, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=966026.7, rms=1.932 (1.906%) 061: dt: 0.1250, sse=960075.4, rms=1.862 (3.597%) rms = 1.85, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=958348.0, rms=1.846 (0.872%) positioning took 0.8 minutes mean border=67.6, 2960 (1) missing vertices, mean dist 0.0 [0.2 (%45.7)->0.2 (%54.3))] %55 local maxima, %14 large gradients and %23 min vals, 136 gradients ignored tol=1.0e-04, sigma=0.2, host=gust., 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 /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=970881.6, rms=1.997 rms = 2.26, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=959126.9, rms=1.869 (6.403%) rms = 1.83, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=954560.5, rms=1.830 (2.078%) rms = 1.78, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=950802.4, rms=1.782 (2.592%) positioning took 0.5 minutes writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/rh.area.pial vertex spacing 1.00 +- 0.43 (0.08-->9.00) (max @ vno 56503 --> 53264) face area 0.39 +- 0.31 (0.00-->9.58) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 131968 vertices processed 25000 of 131968 vertices processed 50000 of 131968 vertices processed 75000 of 131968 vertices processed 100000 of 131968 vertices processed 125000 of 131968 vertices processed 0 of 131968 vertices processed 25000 of 131968 vertices processed 50000 of 131968 vertices processed 75000 of 131968 vertices processed 100000 of 131968 vertices processed 125000 of 131968 vertices processed thickness calculation complete, 404:716 truncations. 31080 vertices at 0 distance 91723 vertices at 1 distance 78475 vertices at 2 distance 33229 vertices at 3 distance 11000 vertices at 4 distance 3657 vertices at 5 distance 1230 vertices at 6 distance 387 vertices at 7 distance 111 vertices at 8 distance 81 vertices at 9 distance 48 vertices at 10 distance 31 vertices at 11 distance 26 vertices at 12 distance 12 vertices at 13 distance 9 vertices at 14 distance 4 vertices at 15 distance 12 vertices at 16 distance 7 vertices at 17 distance 6 vertices at 18 distance 9 vertices at 19 distance 5 vertices at 20 distance writing curvature file /space/freesurfer/subjects/test/bert.Darwin/surf/rh.thickness positioning took 10.8 minutes #-------------------------------------------- #@# Surf Volume lh Wed Jan 27 22:25:59 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/surf /space/freesurfer/subjects/test/bert.Darwin/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume bert.Darwin lh /space/freesurfer/subjects/test/bert.Darwin/surf/lh.volume masking with /space/freesurfer/subjects/test/bert.Darwin/label/lh.cortex.label Total face volume 251085 Total vertex volume 247826 (mask=0) #@# bert.Darwin lh 247826 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed Jan 27 22:26:15 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/surf /space/freesurfer/subjects/test/bert.Darwin/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume bert.Darwin rh /space/freesurfer/subjects/test/bert.Darwin/surf/rh.volume masking with /space/freesurfer/subjects/test/bert.Darwin/label/rh.cortex.label Total face volume 248640 Total vertex volume 244954 (mask=0) #@# bert.Darwin rh 244954 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 27 22:26:24 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon bert.Darwin \n SUBJECTS_DIR is /space/freesurfer/subjects/test 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 = 48 writing volume /space/freesurfer/subjects/test/bert.Darwin/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Wed Jan 27 22:39:30 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab bert.Darwin lh white \n computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 251085 Total vertex volume 247826 (mask=0) 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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1334 920 2456 2.852 0.419 0.103 0.017 9 0.9 bankssts 918 630 1620 2.724 0.519 0.127 0.011 12 0.4 caudalanteriorcingulate 2415 1596 5172 2.848 0.524 0.115 0.021 24 2.0 caudalmiddlefrontal 2462 1553 2907 1.821 0.464 0.146 0.034 36 3.6 cuneus 468 326 1590 3.457 0.645 0.110 0.023 3 0.5 entorhinal 4246 2929 8482 2.712 0.620 0.132 0.026 55 4.8 fusiform 5826 3982 11688 2.700 0.500 0.125 0.027 68 6.2 inferiorparietal 4837 3365 11989 3.053 0.604 0.141 0.031 70 6.3 inferiortemporal 1518 966 2354 2.213 0.763 0.119 0.025 20 1.5 isthmuscingulate 7402 4740 11967 2.306 0.589 0.141 0.036 97 10.5 lateraloccipital 3536 2446 8196 2.937 0.641 0.137 0.029 43 4.4 lateralorbitofrontal 4445 2960 5807 1.900 0.527 0.128 0.028 52 5.4 lingual 3115 2114 6642 2.733 0.946 0.119 0.034 50 4.1 medialorbitofrontal 4534 3081 12016 3.176 0.607 0.131 0.027 61 5.2 middletemporal 964 640 1781 2.532 0.573 0.072 0.011 4 0.4 parahippocampal 2036 1317 3789 2.635 0.597 0.101 0.021 12 1.8 paracentral 2724 1862 6192 2.940 0.503 0.111 0.019 23 2.2 parsopercularis 835 569 2239 3.145 0.533 0.124 0.025 11 0.7 parsorbitalis 2329 1552 4539 2.728 0.517 0.114 0.020 22 1.8 parstriangularis 1935 1269 1801 1.586 0.435 0.127 0.029 21 2.2 pericalcarine 5810 3688 9246 2.243 0.681 0.100 0.021 43 4.5 postcentral 1717 1166 3266 2.540 0.567 0.129 0.023 24 1.6 posteriorcingulate 7293 4538 14825 2.988 0.640 0.103 0.023 55 6.9 precentral 5807 3878 9777 2.433 0.568 0.120 0.025 59 5.7 precuneus 1195 782 2639 3.158 0.490 0.131 0.025 17 1.2 rostralanteriorcingulate 8932 5989 17294 2.572 0.513 0.131 0.029 120 10.3 rostralmiddlefrontal 10005 6865 23672 3.057 0.551 0.119 0.023 97 9.5 superiorfrontal 7716 5053 13658 2.422 0.533 0.121 0.023 84 7.0 superiorparietal 5637 3859 12619 2.935 0.597 0.116 0.022 55 4.9 superiortemporal 7254 4914 15382 2.799 0.549 0.124 0.024 83 7.0 supramarginal 296 204 861 2.792 0.670 0.172 0.071 10 1.0 frontalpole 629 453 2805 3.962 0.560 0.160 0.058 11 1.4 temporalpole 802 519 1295 2.427 0.547 0.139 0.027 11 0.8 transversetemporal 3345 2225 7259 3.248 0.655 0.093 0.019 24 2.6 insula \n mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab bert.Darwin lh pial \n computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 251085 Total vertex volume 247826 (mask=0) 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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1334 798 2456 2.852 0.419 0.108 0.024 17 1.3 bankssts 918 664 1620 2.724 0.519 0.110 0.017 19 0.7 caudalanteriorcingulate 2415 1941 5172 2.848 0.524 0.118 0.021 35 2.2 caudalmiddlefrontal 2462 1753 2907 1.821 0.464 0.135 0.029 38 3.4 cuneus 468 598 1590 3.457 0.645 0.169 0.029 5 0.7 entorhinal 4246 3366 8482 2.712 0.620 0.129 0.028 61 5.5 fusiform 5826 4514 11688 2.700 0.500 0.129 0.027 67 7.0 inferiorparietal 4837 4408 11989 3.053 0.604 0.149 0.033 69 7.4 inferiortemporal 1518 1164 2354 2.213 0.763 0.147 0.036 35 2.1 isthmuscingulate 7402 5643 11967 2.306 0.589 0.127 0.026 92 8.7 lateraloccipital 3536 3032 8196 2.937 0.641 0.151 0.035 59 5.5 lateralorbitofrontal 4445 3342 5807 1.900 0.527 0.130 0.032 61 6.4 lingual 3115 2889 6642 2.733 0.946 0.163 0.041 71 5.7 medialorbitofrontal 4534 4327 12016 3.176 0.607 0.143 0.027 55 5.6 middletemporal 964 796 1781 2.532 0.573 0.106 0.020 6 0.9 parahippocampal 2036 1531 3789 2.635 0.597 0.105 0.018 18 1.6 paracentral 2724 2233 6192 2.940 0.503 0.126 0.024 26 3.0 parsopercularis 835 852 2239 3.145 0.533 0.149 0.030 10 1.1 parsorbitalis 2329 1759 4539 2.728 0.517 0.122 0.024 25 2.5 parstriangularis 1935 1089 1801 1.586 0.435 0.104 0.025 22 2.1 pericalcarine 5810 4555 9246 2.243 0.681 0.114 0.019 48 4.9 postcentral 1717 1354 3266 2.540 0.567 0.144 0.031 73 2.3 posteriorcingulate 7293 5197 14825 2.988 0.640 0.102 0.021 64 6.7 precentral 5807 4129 9777 2.433 0.568 0.124 0.027 81 6.5 precuneus 1195 932 2639 3.158 0.490 0.150 0.032 38 1.7 rostralanteriorcingulate 8932 7156 17294 2.572 0.513 0.134 0.025 114 10.4 rostralmiddlefrontal 10005 8254 23672 3.057 0.551 0.125 0.024 116 10.6 superiorfrontal 7716 6017 13658 2.422 0.533 0.125 0.024 85 8.0 superiorparietal 5637 4500 12619 2.935 0.597 0.126 0.026 88 6.8 superiortemporal 7254 5865 15382 2.799 0.549 0.128 0.025 99 7.9 supramarginal 296 370 861 2.792 0.670 0.189 0.038 4 0.5 frontalpole 629 943 2805 3.962 0.560 0.200 0.037 5 1.1 temporalpole 802 587 1295 2.427 0.547 0.103 0.022 4 0.7 transversetemporal 3345 2068 7259 3.248 0.655 0.110 0.026 39 3.7 insula #----------------------------------------- #@# Parcellation Stats rh Wed Jan 27 22:40:50 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab bert.Darwin rh white \n computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 248640 Total vertex volume 244954 (mask=0) 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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1038 729 1916 2.639 0.497 0.091 0.017 5 0.6 bankssts 1218 817 2469 2.639 0.634 0.134 0.019 17 0.9 caudalanteriorcingulate 2497 1709 5345 2.925 0.481 0.112 0.020 19 2.0 caudalmiddlefrontal 2255 1449 2801 1.876 0.554 0.134 0.031 30 3.1 cuneus 432 320 1630 3.441 0.562 0.127 0.029 4 0.4 entorhinal 4375 3035 8835 2.644 0.599 0.128 0.026 56 4.5 fusiform 7274 4999 15571 2.753 0.463 0.126 0.026 88 7.7 inferiorparietal 4317 3006 10695 3.009 0.626 0.139 0.033 63 6.0 inferiortemporal 1171 772 2028 2.407 0.756 0.123 0.029 16 1.1 isthmuscingulate 8328 5483 12924 2.209 0.551 0.137 0.032 108 10.9 lateraloccipital 3606 2544 8317 3.014 0.650 0.133 0.032 46 4.6 lateralorbitofrontal 4275 2850 6131 2.033 0.574 0.131 0.034 55 5.7 lingual 2892 2052 5734 2.646 0.687 0.129 0.025 39 3.1 medialorbitofrontal 4726 3290 11475 2.921 0.612 0.133 0.030 64 6.0 middletemporal 1034 679 1940 2.626 0.601 0.084 0.016 7 0.5 parahippocampal 2288 1498 4018 2.539 0.462 0.114 0.031 28 3.3 paracentral 1988 1332 4219 2.986 0.437 0.117 0.024 18 1.8 parsopercularis 1373 900 3407 2.985 0.628 0.133 0.027 17 1.6 parsorbitalis 2686 1792 5376 2.668 0.475 0.117 0.023 29 2.3 parstriangularis 2028 1311 2045 1.779 0.530 0.112 0.025 14 1.9 pericalcarine 6076 3813 9489 2.244 0.662 0.102 0.021 47 5.2 postcentral 1773 1261 3541 2.535 0.642 0.137 0.026 25 1.9 posteriorcingulate 7578 4663 14967 2.896 0.639 0.103 0.021 57 6.6 precentral 6099 4063 10662 2.530 0.512 0.115 0.023 61 5.5 precuneus 995 666 2352 3.042 0.564 0.136 0.025 15 1.0 rostralanteriorcingulate 8640 5734 17251 2.635 0.505 0.129 0.029 105 10.2 rostralmiddlefrontal 8988 6124 21223 3.077 0.540 0.121 0.025 84 9.0 superiorfrontal 7895 5173 14113 2.435 0.526 0.119 0.022 83 6.7 superiorparietal 5214 3505 11469 2.957 0.561 0.109 0.022 48 4.8 superiortemporal 5572 3807 11273 2.759 0.522 0.125 0.025 63 6.2 supramarginal 506 346 1240 2.638 0.482 0.153 0.032 9 0.7 frontalpole 478 356 2103 3.969 0.551 0.167 0.043 7 0.8 temporalpole 552 327 896 2.551 0.503 0.115 0.020 5 0.4 transversetemporal 3534 2344 7496 3.220 0.827 0.110 0.027 36 4.3 insula \n mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab bert.Darwin rh pial \n computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 248640 Total vertex volume 244954 (mask=0) 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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1038 687 1916 2.639 0.497 0.114 0.023 13 1.1 bankssts 1218 1016 2469 2.639 0.634 0.176 0.041 159 1.7 caudalanteriorcingulate 2497 1826 5345 2.925 0.481 0.114 0.022 32 2.5 caudalmiddlefrontal 2255 1669 2801 1.876 0.554 0.123 0.026 27 2.6 cuneus 432 578 1630 3.441 0.562 0.160 0.023 6 0.5 entorhinal 4375 3526 8835 2.644 0.599 0.138 0.036 68 6.1 fusiform 7274 6067 15571 2.753 0.463 0.131 0.025 73 8.2 inferiorparietal 4317 4006 10695 3.009 0.626 0.149 0.033 71 7.2 inferiortemporal 1171 858 2028 2.407 0.756 0.132 0.029 28 1.5 isthmuscingulate 8328 6273 12924 2.209 0.551 0.132 0.028 129 10.5 lateraloccipital 3606 2994 8317 3.014 0.650 0.149 0.038 57 5.7 lateralorbitofrontal 4275 3230 6131 2.033 0.574 0.126 0.032 64 6.3 lingual 2892 2400 5734 2.646 0.687 0.134 0.026 31 3.4 medialorbitofrontal 4726 4462 11475 2.921 0.612 0.152 0.030 60 6.8 middletemporal 1034 812 1940 2.626 0.601 0.115 0.022 9 1.0 parahippocampal 2288 1608 4018 2.539 0.462 0.108 0.020 24 2.1 paracentral 1988 1445 4219 2.986 0.437 0.111 0.023 21 2.0 parsopercularis 1373 1332 3407 2.985 0.628 0.143 0.028 14 1.8 parsorbitalis 2686 2181 5376 2.668 0.475 0.120 0.019 26 2.2 parstriangularis 2028 1140 2045 1.779 0.530 0.102 0.024 26 2.0 pericalcarine 6076 4553 9489 2.244 0.662 0.111 0.021 58 5.5 postcentral 1773 1431 3541 2.535 0.642 0.137 0.028 41 2.1 posteriorcingulate 7578 5422 14967 2.896 0.639 0.096 0.018 65 5.9 precentral 6099 4369 10662 2.530 0.512 0.116 0.024 105 5.9 precuneus 995 908 2352 3.042 0.564 0.166 0.033 41 1.6 rostralanteriorcingulate 8640 7068 17251 2.635 0.505 0.135 0.025 96 9.8 rostralmiddlefrontal 8988 7396 21223 3.077 0.540 0.128 0.026 120 9.6 superiorfrontal 7895 6117 14113 2.435 0.526 0.123 0.023 81 7.6 superiorparietal 5214 4240 11469 2.957 0.561 0.120 0.023 58 5.4 superiortemporal 5572 4249 11273 2.759 0.522 0.127 0.027 70 6.6 supramarginal 506 572 1240 2.638 0.482 0.179 0.026 6 0.6 frontalpole 478 697 2103 3.969 0.551 0.214 0.044 7 0.9 temporalpole 552 387 896 2.551 0.503 0.101 0.019 3 0.5 transversetemporal 3534 2144 7496 3.220 0.827 0.117 0.031 73 4.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Jan 27 22:42:07 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert.Darwin lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot \n setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 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... 78 labels changed using aseg relabeling using gibbs priors... 000: 9100 changed, 133016 examined... 001: 2225 changed, 35156 examined... 002: 673 changed, 11539 examined... 003: 278 changed, 3804 examined... 004: 147 changed, 1587 examined... 005: 71 changed, 812 examined... 006: 33 changed, 395 examined... 007: 13 changed, 172 examined... 008: 9 changed, 84 examined... 009: 5 changed, 50 examined... 010: 2 changed, 26 examined... 011: 0 changed, 13 examined... 27 labels changed using aseg 000: 311 total segments, 225 labels (2455 vertices) changed 001: 99 total segments, 16 labels (49 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 52 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1022 vertices marked for relabeling... 1022 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 29 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Wed Jan 27 22:42:38 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert.Darwin rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot \n setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 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... 57 labels changed using aseg relabeling using gibbs priors... 000: 9293 changed, 131968 examined... 001: 2190 changed, 35827 examined... 002: 726 changed, 11410 examined... 003: 322 changed, 3989 examined... 004: 151 changed, 1777 examined... 005: 85 changed, 836 examined... 006: 43 changed, 457 examined... 007: 19 changed, 257 examined... 008: 11 changed, 105 examined... 009: 8 changed, 53 examined... 010: 2 changed, 42 examined... 011: 2 changed, 13 examined... 012: 2 changed, 14 examined... 013: 1 changed, 10 examined... 014: 0 changed, 7 examined... 19 labels changed using aseg 000: 295 total segments, 209 labels (2038 vertices) changed 001: 106 total segments, 20 labels (58 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 31 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 622 vertices marked for relabeling... 622 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 29 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jan 27 22:43:08 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_anatomical_stats -th3 -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 bert.Darwin lh white \n computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 251085 Total vertex volume 247826 (mask=0) 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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1259 854 2385 2.493 0.498 0.140 0.030 18 1.6 G_and_S_frontomargin 1791 1188 2967 2.346 0.573 0.150 0.035 27 2.4 G_and_S_occipital_inf 1662 948 3122 2.683 0.569 0.104 0.024 14 1.6 G_and_S_paracentral 1330 886 3199 3.041 0.548 0.139 0.031 19 1.7 G_and_S_subcentral 790 500 1751 2.594 0.522 0.147 0.043 15 1.3 G_and_S_transv_frontopol 2279 1548 4992 2.968 0.463 0.114 0.021 23 1.9 G_and_S_cingul-Ant 1447 1020 2933 2.860 0.553 0.113 0.016 11 1.0 G_and_S_cingul-Mid-Ant 1283 913 2394 2.598 0.418 0.108 0.018 10 0.9 G_and_S_cingul-Mid-Post 511 344 1358 3.016 0.445 0.160 0.039 11 0.7 G_cingul-Post-dorsal 359 217 488 1.926 0.753 0.132 0.030 6 0.5 G_cingul-Post-ventral 2176 1351 2532 1.722 0.424 0.142 0.035 31 3.2 G_cuneus 1349 934 3730 3.112 0.501 0.125 0.025 16 1.3 G_front_inf-Opercular 293 199 800 2.891 0.384 0.134 0.026 6 0.2 G_front_inf-Orbital 1419 952 3557 2.989 0.459 0.137 0.026 21 1.4 G_front_inf-Triangul 3899 2632 10084 2.900 0.527 0.141 0.034 63 5.2 G_front_middle 6698 4573 17668 3.193 0.531 0.131 0.028 77 7.5 G_front_sup 527 339 1445 3.701 0.612 0.095 0.020 5 0.4 G_Ins_lg_and_S_cent_ins 760 492 2405 3.607 0.638 0.105 0.027 9 0.9 G_insular_short 2058 1389 4586 2.738 0.494 0.148 0.036 34 2.7 G_occipital_middle 1450 960 2714 2.377 0.559 0.128 0.026 17 1.4 G_occipital_sup 1854 1263 4436 2.898 0.585 0.145 0.030 33 2.2 G_oc-temp_lat-fusifor 3010 1940 3913 1.826 0.535 0.139 0.035 43 4.5 G_oc-temp_med-Lingual 1014 679 2621 3.013 0.703 0.095 0.019 7 0.7 G_oc-temp_med-Parahip 2260 1586 6655 3.203 0.656 0.141 0.029 30 3.1 G_orbital 2507 1759 6559 2.920 0.451 0.148 0.031 42 3.2 G_pariet_inf-Angular 3679 2510 8732 2.898 0.563 0.129 0.027 46 3.9 G_pariet_inf-Supramar 3301 2162 6987 2.554 0.599 0.134 0.028 46 3.8 G_parietal_sup 2109 1254 3606 2.282 0.559 0.100 0.024 17 1.9 G_postcentral 2896 1647 7100 3.212 0.649 0.102 0.028 27 3.3 G_precentral 2578 1716 5195 2.458 0.546 0.131 0.028 36 2.8 G_precuneus 1013 725 3065 2.802 0.639 0.141 0.044 30 2.2 G_rectus 424 274 680 2.901 1.543 0.113 0.060 6 0.8 G_subcallosal 603 399 1180 2.582 0.604 0.152 0.030 9 0.7 G_temp_sup-G_T_transv 2204 1541 6760 3.218 0.570 0.142 0.032 32 2.8 G_temp_sup-Lateral 472 333 1379 3.637 0.614 0.099 0.026 3 0.3 G_temp_sup-Plan_polar 1172 780 2529 2.840 0.579 0.118 0.019 14 0.9 G_temp_sup-Plan_tempo 3029 2121 8693 3.117 0.575 0.155 0.037 57 4.8 G_temporal_inf 2693 1831 8165 3.292 0.560 0.148 0.034 47 3.9 G_temporal_middle 407 269 563 2.372 0.368 0.087 0.012 1 0.2 Lat_Fis-ant-Horizont 391 264 630 2.908 0.408 0.107 0.019 2 0.3 Lat_Fis-ant-Vertical 1459 959 2091 2.840 0.544 0.111 0.020 10 1.2 Lat_Fis-post 2349 1376 3031 1.986 0.572 0.140 0.043 30 4.2 Pole_occipital 1476 1069 5541 3.545 0.747 0.151 0.044 22 2.8 Pole_temporal 2564 1740 2859 1.858 0.622 0.118 0.023 23 2.3 S_calcarine 3076 2074 3924 2.145 0.709 0.089 0.016 12 1.9 S_central 1067 724 1567 2.369 0.464 0.089 0.012 5 0.5 S_cingul-Marginalis 511 331 849 2.981 0.401 0.110 0.020 3 0.4 S_circular_insula_ant 1583 1055 2516 2.921 0.567 0.084 0.013 8 0.9 S_circular_insula_inf 1899 1293 3021 2.899 0.413 0.087 0.013 6 1.1 S_circular_insula_sup 555 401 1244 3.031 0.786 0.131 0.026 7 0.6 S_collat_transv_ant 357 250 448 1.920 0.404 0.135 0.029 3 0.5 S_collat_transv_post 2813 1859 4745 2.483 0.517 0.106 0.018 25 2.0 S_front_inf 1585 1055 2247 2.294 0.390 0.114 0.025 13 1.5 S_front_middle 2373 1634 4374 2.703 0.437 0.098 0.015 17 1.4 S_front_sup 667 465 1033 2.573 0.361 0.090 0.011 3 0.3 S_interm_prim-Jensen 3277 2184 5097 2.432 0.479 0.109 0.018 26 2.4 S_intrapariet_and_P_trans 1195 803 1549 2.268 0.514 0.122 0.028 9 1.4 S_oc_middle_and_Lunatus 769 508 951 2.157 0.401 0.091 0.013 4 0.4 S_oc_sup_and_transversal 532 352 811 2.558 0.400 0.119 0.020 4 0.5 S_occipital_ant 996 684 1621 2.683 0.369 0.099 0.015 5 0.6 S_oc-temp_lat 2076 1449 3013 2.341 0.371 0.098 0.013 12 1.1 S_oc-temp_med_and_Lingual 434 285 625 2.591 0.469 0.118 0.024 5 0.4 S_orbital_lateral 651 467 1197 2.490 0.736 0.102 0.014 4 0.4 S_orbital_med-olfact 1263 871 2277 2.674 0.550 0.134 0.033 14 1.6 S_orbital-H_Shaped 2585 1686 3564 2.331 0.590 0.115 0.022 22 2.3 S_parieto_occipital 1215 712 1080 2.176 0.901 0.130 0.019 25 0.8 S_pericallosal 2801 1833 3721 2.169 0.444 0.108 0.021 21 2.2 S_postcentral 1458 986 2275 2.740 0.465 0.109 0.019 9 1.2 S_precentral-inf-part 1148 772 1839 2.862 0.462 0.099 0.019 6 0.9 S_precentral-sup-part 1103 741 1864 2.769 0.889 0.128 0.026 14 1.1 S_suborbital 903 593 1464 2.532 0.492 0.126 0.030 9 1.1 S_subparietal 1223 819 1835 2.945 0.618 0.116 0.021 7 1.2 S_temporal_inf 4978 3359 8473 2.728 0.438 0.106 0.019 39 3.6 S_temporal_sup 420 270 527 2.312 0.590 0.121 0.023 5 0.4 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Wed Jan 27 22:43:47 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_anatomical_stats -th3 -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 bert.Darwin rh white \n computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 248640 Total vertex volume 244954 (mask=0) 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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1193 795 2395 2.618 0.533 0.138 0.040 17 1.9 G_and_S_frontomargin 1418 962 2479 2.456 0.515 0.131 0.029 17 1.7 G_and_S_occipital_inf 1435 858 2450 2.475 0.507 0.114 0.026 13 1.4 G_and_S_paracentral 1134 804 2758 3.032 0.499 0.142 0.032 15 1.3 G_and_S_subcentral 1151 771 2690 2.710 0.526 0.145 0.030 19 1.5 G_and_S_transv_frontopol 3134 2124 6337 2.926 0.496 0.121 0.023 33 2.8 G_and_S_cingul-Ant 1379 981 3120 2.873 0.480 0.115 0.020 12 1.2 G_and_S_cingul-Mid-Ant 1400 1005 2745 2.644 0.397 0.113 0.021 11 1.3 G_and_S_cingul-Mid-Post 433 313 1278 3.066 0.411 0.155 0.038 8 0.6 G_cingul-Post-dorsal 296 190 678 2.742 0.702 0.153 0.032 6 0.4 G_cingul-Post-ventral 2116 1362 2563 1.751 0.485 0.133 0.030 28 2.7 G_cuneus 1155 757 3089 3.172 0.359 0.130 0.027 14 1.3 G_front_inf-Opercular 468 304 1273 2.978 0.433 0.149 0.031 9 0.6 G_front_inf-Orbital 1424 927 3465 2.865 0.423 0.134 0.029 22 1.6 G_front_inf-Triangul 3834 2571 9913 2.905 0.487 0.141 0.031 58 5.0 G_front_middle 5962 3997 15969 3.173 0.549 0.129 0.031 78 8.0 G_front_sup 526 349 1448 3.738 0.749 0.104 0.022 5 0.4 G_Ins_lg_and_S_cent_ins 706 457 2241 3.706 0.743 0.122 0.027 11 0.8 G_insular_short 2387 1595 5477 2.661 0.497 0.149 0.039 44 3.7 G_occipital_middle 1672 1106 3061 2.271 0.528 0.126 0.028 19 1.7 G_occipital_sup 2063 1427 4699 2.605 0.490 0.144 0.033 37 3.0 G_oc-temp_lat-fusifor 2847 1824 4492 2.106 0.623 0.144 0.039 47 4.6 G_oc-temp_med-Lingual 1291 863 3161 2.994 0.777 0.122 0.036 16 1.8 G_oc-temp_med-Parahip 2576 1805 7840 3.274 0.642 0.145 0.035 42 3.6 G_orbital 2731 1898 7379 2.947 0.443 0.149 0.034 47 3.7 G_pariet_inf-Angular 2804 1941 6849 2.964 0.446 0.146 0.033 46 4.3 G_pariet_inf-Supramar 2564 1660 5731 2.629 0.529 0.128 0.025 36 2.3 G_parietal_sup 2313 1293 3874 2.306 0.634 0.101 0.024 21 2.3 G_postcentral 3099 1722 7437 3.223 0.586 0.099 0.022 27 2.7 G_precentral 3194 2119 6334 2.484 0.504 0.126 0.026 44 3.2 G_precuneus 760 615 1941 2.457 0.744 0.159 0.036 15 1.3 G_rectus 135 103 340 3.241 0.479 0.069 0.018 1 0.0 G_subcallosal 435 255 835 2.663 0.511 0.125 0.026 5 0.4 G_temp_sup-G_T_transv 1748 1171 5090 3.231 0.514 0.141 0.034 27 2.3 G_temp_sup-Lateral 590 406 1525 3.477 0.681 0.093 0.023 2 0.5 G_temp_sup-Plan_polar 700 485 1452 2.811 0.554 0.093 0.023 4 0.6 G_temp_sup-Plan_tempo 2774 1950 7663 3.017 0.594 0.152 0.039 51 4.5 G_temporal_inf 2633 1865 7855 3.131 0.545 0.148 0.036 46 4.2 G_temporal_middle 508 347 647 2.272 0.351 0.086 0.010 2 0.2 Lat_Fis-ant-Horizont 234 165 387 2.747 0.462 0.113 0.023 1 0.2 Lat_Fis-ant-Vertical 1521 1017 2137 2.609 0.630 0.098 0.015 8 0.9 Lat_Fis-post 3486 2118 4038 1.850 0.515 0.143 0.038 50 5.3 Pole_occipital 1361 1006 5268 3.672 0.672 0.161 0.038 22 2.1 Pole_temporal 2272 1583 2575 1.915 0.583 0.113 0.024 17 2.1 S_calcarine 3081 2012 3844 2.180 0.722 0.093 0.018 15 2.4 S_central 1438 972 2251 2.531 0.481 0.097 0.016 8 0.9 S_cingul-Marginalis 634 422 1083 3.217 0.464 0.102 0.018 3 0.5 S_circular_insula_ant 1371 884 1986 2.788 0.639 0.087 0.020 7 1.6 S_circular_insula_inf 1487 1030 2468 2.766 0.480 0.088 0.013 5 0.8 S_circular_insula_sup 710 480 1355 2.752 0.708 0.118 0.019 7 0.5 S_collat_transv_ant 535 360 691 2.180 0.448 0.146 0.034 6 0.8 S_collat_transv_post 2123 1414 3235 2.548 0.437 0.108 0.023 15 1.9 S_front_inf 1999 1328 2972 2.423 0.373 0.109 0.020 15 1.4 S_front_middle 1946 1362 3697 2.762 0.567 0.112 0.020 14 1.5 S_front_sup 694 474 983 2.456 0.418 0.102 0.013 4 0.4 S_interm_prim-Jensen 3027 2016 4624 2.521 0.473 0.112 0.019 24 2.2 S_intrapariet_and_P_trans 1290 904 1867 2.395 0.416 0.118 0.021 9 1.1 S_oc_middle_and_Lunatus 1270 870 1465 1.980 0.439 0.106 0.019 8 0.9 S_oc_sup_and_transversal 803 529 1180 2.525 0.442 0.107 0.021 5 0.8 S_occipital_ant 757 521 1276 2.832 0.566 0.110 0.020 5 0.6 S_oc-temp_lat 2034 1428 2971 2.457 0.437 0.093 0.013 10 1.0 S_oc-temp_med_and_Lingual 538 350 656 2.351 0.524 0.113 0.017 4 0.4 S_orbital_lateral 765 544 1201 2.374 0.658 0.104 0.012 5 0.4 S_orbital_med-olfact 1452 1013 2611 2.741 0.565 0.129 0.035 16 2.1 S_orbital-H_Shaped 2298 1540 3501 2.575 0.520 0.107 0.021 15 2.0 S_parieto_occipital 1548 955 1451 2.102 0.738 0.133 0.020 26 1.0 S_pericallosal 2638 1780 3861 2.345 0.475 0.099 0.015 15 1.6 S_postcentral 1925 1261 3075 2.732 0.360 0.097 0.015 10 1.2 S_precentral-inf-part 1181 810 1707 2.508 0.435 0.125 0.022 10 1.2 S_precentral-sup-part 326 227 649 2.928 0.707 0.122 0.016 3 0.3 S_suborbital 819 540 1397 2.590 0.575 0.113 0.021 7 0.7 S_subparietal 1354 920 2208 2.656 0.457 0.123 0.022 11 1.4 S_temporal_inf 5451 3716 9172 2.555 0.423 0.095 0.015 34 3.3 S_temporal_sup 345 224 539 3.000 0.487 0.096 0.011 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Jan 27 22:44:27 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert.Darwin lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot \n setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1500 labels changed using aseg relabeling using gibbs priors... 000: 2692 changed, 133016 examined... 001: 634 changed, 11413 examined... 002: 155 changed, 3424 examined... 003: 66 changed, 918 examined... 004: 32 changed, 392 examined... 005: 10 changed, 174 examined... 006: 5 changed, 64 examined... 007: 3 changed, 31 examined... 008: 2 changed, 19 examined... 009: 2 changed, 10 examined... 010: 2 changed, 11 examined... 011: 1 changed, 10 examined... 012: 2 changed, 6 examined... 013: 1 changed, 12 examined... 014: 1 changed, 7 examined... 015: 0 changed, 7 examined... 142 labels changed using aseg 000: 66 total segments, 33 labels (282 vertices) changed 001: 35 total segments, 2 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 829 vertices marked for relabeling... 829 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Wed Jan 27 22:44:47 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert.Darwin rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot \n setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1437 labels changed using aseg relabeling using gibbs priors... 000: 2615 changed, 131968 examined... 001: 625 changed, 10994 examined... 002: 180 changed, 3469 examined... 003: 72 changed, 1064 examined... 004: 37 changed, 393 examined... 005: 21 changed, 199 examined... 006: 10 changed, 114 examined... 007: 10 changed, 64 examined... 008: 7 changed, 56 examined... 009: 10 changed, 37 examined... 010: 9 changed, 39 examined... 011: 10 changed, 39 examined... 012: 2 changed, 42 examined... 013: 1 changed, 12 examined... 014: 1 changed, 7 examined... 015: 1 changed, 7 examined... 016: 0 changed, 8 examined... 230 labels changed using aseg 000: 72 total segments, 39 labels (344 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 434 vertices marked for relabeling... 434 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Jan 27 22:45:07 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab bert.Darwin lh white \n computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 251085 Total vertex volume 247826 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1648 1142 3271 2.821 0.493 0.118 0.014 18 0.8 caudalanteriorcingulate 2619 1726 5627 2.865 0.516 0.115 0.021 26 2.2 caudalmiddlefrontal 3487 2236 4503 1.948 0.532 0.136 0.031 45 4.4 cuneus 449 317 1595 3.514 0.615 0.114 0.023 4 0.4 entorhinal 3998 2749 7659 2.664 0.609 0.129 0.024 49 4.1 fusiform 5598 3839 11286 2.693 0.503 0.126 0.027 66 6.1 inferiorparietal 4847 3368 12286 3.055 0.603 0.143 0.033 74 6.8 inferiortemporal 1497 959 2358 2.223 0.759 0.120 0.025 20 1.5 isthmuscingulate 7606 4875 12316 2.306 0.591 0.140 0.036 99 10.7 lateraloccipital 3887 2707 9274 2.947 0.678 0.141 0.033 54 5.3 lateralorbitofrontal 4442 2952 5779 1.893 0.526 0.127 0.028 52 5.3 lingual 2237 1553 5198 2.713 0.861 0.117 0.032 39 2.9 medialorbitofrontal 5628 3819 13926 3.114 0.608 0.126 0.026 67 6.2 middletemporal 969 646 1792 2.525 0.574 0.073 0.011 4 0.4 parahippocampal 2283 1502 4344 2.656 0.585 0.099 0.020 13 1.9 paracentral 2350 1598 5382 2.923 0.507 0.111 0.019 21 1.9 parsopercularis 1094 737 2365 2.808 0.475 0.107 0.018 10 0.8 parsorbitalis 2971 1984 5925 2.759 0.519 0.115 0.021 31 2.4 parstriangularis 1897 1250 1785 1.603 0.454 0.127 0.028 21 2.1 pericalcarine 6546 4178 10336 2.243 0.671 0.104 0.022 52 5.4 postcentral 1850 1256 3402 2.524 0.586 0.128 0.022 25 1.7 posteriorcingulate 7217 4484 14595 2.984 0.640 0.103 0.023 54 6.9 precentral 5484 3650 9428 2.453 0.551 0.121 0.025 57 5.4 precuneus 1658 1082 3218 2.970 0.858 0.132 0.029 24 2.0 rostralanteriorcingulate 5858 3944 11447 2.630 0.546 0.130 0.029 77 6.6 rostralmiddlefrontal 11606 7861 26736 2.953 0.599 0.124 0.026 128 12.5 superiorfrontal 6177 4052 11139 2.466 0.529 0.121 0.024 68 5.8 superiorparietal 7433 5111 17704 3.014 0.642 0.119 0.024 77 7.0 superiortemporal 7101 4797 14962 2.811 0.550 0.123 0.024 80 6.7 supramarginal 789 510 1269 2.421 0.545 0.138 0.027 10 0.8 transversetemporal 3091 2067 6918 3.270 0.645 0.094 0.018 23 2.4 insula #----------------------------------------- #@# Parcellation Stats 3 rh Wed Jan 27 22:45:45 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab bert.Darwin rh white \n computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 248640 Total vertex volume 244954 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1223 821 2475 2.642 0.634 0.135 0.019 18 1.0 caudalanteriorcingulate 2503 1711 5327 2.910 0.494 0.113 0.020 20 1.9 caudalmiddlefrontal 2862 1840 3727 1.987 0.570 0.129 0.029 35 3.5 cuneus 478 348 1703 3.438 0.532 0.125 0.029 4 0.5 entorhinal 3834 2648 7250 2.609 0.562 0.126 0.026 48 3.9 fusiform 6872 4719 14651 2.757 0.459 0.128 0.027 85 7.4 inferiorparietal 4774 3332 12204 3.001 0.644 0.140 0.032 69 6.5 inferiortemporal 1193 787 2061 2.412 0.754 0.123 0.028 16 1.1 isthmuscingulate 8597 5653 13308 2.213 0.555 0.137 0.032 112 11.2 lateraloccipital 4063 2863 9751 3.009 0.658 0.142 0.036 60 6.0 lateralorbitofrontal 4279 2853 6135 2.033 0.574 0.132 0.034 56 5.8 lingual 2206 1609 4655 2.645 0.745 0.134 0.028 32 2.5 medialorbitofrontal 5452 3789 12873 2.891 0.606 0.128 0.028 69 6.4 middletemporal 1040 683 1941 2.619 0.598 0.083 0.015 6 0.5 parahippocampal 2375 1560 4234 2.545 0.468 0.114 0.031 29 3.4 paracentral 2057 1369 4283 2.978 0.436 0.117 0.024 18 1.8 parsopercularis 1527 1001 3547 2.992 0.530 0.123 0.025 17 1.6 parsorbitalis 2838 1896 5590 2.672 0.476 0.121 0.025 32 2.7 parstriangularis 2031 1313 2048 1.782 0.533 0.112 0.025 14 1.9 pericalcarine 6682 4218 10567 2.267 0.660 0.103 0.021 53 5.8 postcentral 1821 1300 3620 2.548 0.634 0.136 0.026 25 1.9 posteriorcingulate 7374 4533 14814 2.917 0.634 0.102 0.021 55 6.5 precentral 6080 4065 10692 2.513 0.515 0.117 0.023 63 5.7 precuneus 1135 764 2523 2.990 0.558 0.133 0.023 16 1.1 rostralanteriorcingulate 5500 3653 11226 2.612 0.521 0.129 0.028 64 6.1 rostralmiddlefrontal 12421 8373 27485 2.937 0.566 0.121 0.025 124 12.6 superiorfrontal 6781 4445 12380 2.459 0.519 0.118 0.021 72 5.4 superiorparietal 6751 4614 15638 3.004 0.635 0.114 0.025 65 7.0 superiortemporal 5014 3418 10107 2.759 0.542 0.122 0.024 55 5.3 supramarginal 539 320 866 2.533 0.496 0.114 0.020 5 0.4 transversetemporal 3399 2250 7273 3.213 0.792 0.106 0.024 33 3.8 insula #----------------------------------------- #@# WM/GM Contrast lh Wed Jan 27 22:46:23 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n pctsurfcon --s bert.Darwin --lh-only \n Log file is /space/freesurfer/subjects/test/bert.Darwin/scripts/pctsurfcon.log Wed Jan 27 22:46:25 EST 2016 setenv SUBJECTS_DIR /space/freesurfer/subjects/test cd /space/freesurfer/subjects/test/bert.Darwin/scripts /usr/local/freesurfer/dev/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Darwin gust.nmr.mgh.harvard.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 i386 FREESURFER_HOME /usr/local/freesurfer/dev mri_vol2surf --mov /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.80933/lh.wm.mgh --regheader bert.Darwin --cortex srcvol = /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /space/freesurfer/subjects/test/bert.Darwin/label/lh.cortex.label Reading surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 74461 Masking with /space/freesurfer/subjects/test/bert.Darwin/label/lh.cortex.label Writing to /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.80933/lh.wm.mgh Dim: 133016 1 1 mri_vol2surf --mov /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.80933/lh.gm.mgh --projfrac 0.3 --regheader bert.Darwin --cortex srcvol = /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /space/freesurfer/subjects/test/bert.Darwin/label/lh.cortex.label Reading surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Done reading source surface Reading thickness /space/freesurfer/subjects/test/bert.Darwin/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 87703 Masking with /space/freesurfer/subjects/test/bert.Darwin/label/lh.cortex.label Writing to /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.80933/lh.gm.mgh Dim: 133016 1 1 mri_concat /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.80933/lh.wm.mgh /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.80933/lh.gm.mgh --paired-diff-norm --mul 100 --o /space/freesurfer/subjects/test/bert.Darwin/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /space/freesurfer/subjects/test/bert.Darwin/surf/lh.w-g.pct.mgh mri_segstats --in /space/freesurfer/subjects/test/bert.Darwin/surf/lh.w-g.pct.mgh --annot bert.Darwin lh aparc --sum /space/freesurfer/subjects/test/bert.Darwin/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --in /space/freesurfer/subjects/test/bert.Darwin/surf/lh.w-g.pct.mgh --annot bert.Darwin lh aparc --sum /space/freesurfer/subjects/test/bert.Darwin/stats/lh.w-g.pct.stats --snr sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman UseRobust 0 Constructing seg from annotation Reading annotation /space/freesurfer/subjects/test/bert.Darwin/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) Seg base 1000 Loading /space/freesurfer/subjects/test/bert.Darwin/surf/lh.w-g.pct.mgh Vertex Area is 0.666329 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Wed Jan 27 22:46:43 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/scripts \n pctsurfcon --s bert.Darwin --rh-only \n Log file is /space/freesurfer/subjects/test/bert.Darwin/scripts/pctsurfcon.log Wed Jan 27 22:46:43 EST 2016 setenv SUBJECTS_DIR /space/freesurfer/subjects/test cd /space/freesurfer/subjects/test/bert.Darwin/scripts /usr/local/freesurfer/dev/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Darwin gust.nmr.mgh.harvard.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 i386 FREESURFER_HOME /usr/local/freesurfer/dev mri_vol2surf --mov /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.81025/rh.wm.mgh --regheader bert.Darwin --cortex srcvol = /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /space/freesurfer/subjects/test/bert.Darwin/label/rh.cortex.label Reading surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 73886 Masking with /space/freesurfer/subjects/test/bert.Darwin/label/rh.cortex.label Writing to /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.81025/rh.wm.mgh Dim: 131968 1 1 mri_vol2surf --mov /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.81025/rh.gm.mgh --projfrac 0.3 --regheader bert.Darwin --cortex srcvol = /space/freesurfer/subjects/test/bert.Darwin/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /space/freesurfer/subjects/test/bert.Darwin/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /space/freesurfer/subjects/test/bert.Darwin/label/rh.cortex.label Reading surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Done reading source surface Reading thickness /space/freesurfer/subjects/test/bert.Darwin/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 87438 Masking with /space/freesurfer/subjects/test/bert.Darwin/label/rh.cortex.label Writing to /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.81025/rh.gm.mgh Dim: 131968 1 1 mri_concat /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.81025/rh.wm.mgh /space/freesurfer/subjects/test/bert.Darwin/surf/tmp.pctsurfcon.81025/rh.gm.mgh --paired-diff-norm --mul 100 --o /space/freesurfer/subjects/test/bert.Darwin/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /space/freesurfer/subjects/test/bert.Darwin/surf/rh.w-g.pct.mgh mri_segstats --in /space/freesurfer/subjects/test/bert.Darwin/surf/rh.w-g.pct.mgh --annot bert.Darwin rh aparc --sum /space/freesurfer/subjects/test/bert.Darwin/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --in /space/freesurfer/subjects/test/bert.Darwin/surf/rh.w-g.pct.mgh --annot bert.Darwin rh aparc --sum /space/freesurfer/subjects/test/bert.Darwin/stats/rh.w-g.pct.stats --snr sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman UseRobust 0 Constructing seg from annotation Reading annotation /space/freesurfer/subjects/test/bert.Darwin/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) Seg base 2000 Loading /space/freesurfer/subjects/test/bert.Darwin/surf/rh.w-g.pct.mgh Vertex Area is 0.670311 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Wed Jan 27 22:46:53 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz \n reading input surface ../surf/lh.white... relabeling lh hypointensities... 316 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 180 voxels changed to hypointensity... 443 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg Wed Jan 27 22:47:23 EST 2016 /space/freesurfer/subjects/test/bert.Darwin \n mri_aparc2aseg --s bert.Darwin --volmask --aseg aseg.presurf.hypos \n SUBJECTS_DIR /space/freesurfer/subjects/test subject bert.Darwin outvol /space/freesurfer/subjects/test/bert.Darwin/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading lh pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial Loading lh annotations from /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading rh pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial Loading rh annotations from /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 490205 Used brute-force search on 0 voxels Writing output aseg to /space/freesurfer/subjects/test/bert.Darwin/mri/aparc+aseg.mgz \n mri_aparc2aseg --s bert.Darwin --volmask --aseg aseg.presurf.hypos --a2009s \n SUBJECTS_DIR /space/freesurfer/subjects/test subject bert.Darwin outvol /space/freesurfer/subjects/test/bert.Darwin/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading lh pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial Loading lh annotations from /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading rh pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial Loading rh annotations from /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 490205 Used brute-force search on 0 voxels Writing output aseg to /space/freesurfer/subjects/test/bert.Darwin/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Wed Jan 27 22:50:25 EST 2016 /space/freesurfer/subjects/test/bert.Darwin/mri \n apas2aseg --i aparc+aseg.mgz --o aseg.mgz \n Wed Jan 27 22:50:26 EST 2016 setenv SUBJECTS_DIR /space/freesurfer/subjects/test cd /space/freesurfer/subjects/test/bert.Darwin/mri /usr/local/freesurfer/dev/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Darwin-OSX-dev-20160126 $Id: apas2aseg,v 1.1 2014/08/14 22:25:53 greve Exp $ Darwin gust.nmr.mgh.harvard.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 i386 mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/mri cmdline mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Wed Jan 27 22:50:26 EST 2016 Ended at Wed Jan 27 22:50:35 EST 2016 Apas2aseg-Run-Time-Sec 8 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed Jan 27 22:50:35 EST 2016 /space/freesurfer/subjects/test/bert.Darwin \n mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --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 --euler --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject bert.Darwin \n $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --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 --euler --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject bert.Darwin sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman UseRobust 0 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) Computing euler number orig.nofix lheno = -70, rheno = -66 orig.nofix lhholes = 36, rhholes = 34 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 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 Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Wed Jan 27 22:54:26 EST 2016 /space/freesurfer/subjects/test/bert.Darwin \n mri_aparc2aseg --s bert.Darwin --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz \n SUBJECTS_DIR /space/freesurfer/subjects/test subject bert.Darwin outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /space/freesurfer/subjects/test/bert.Darwin/mri/aparc+aseg.mgz Reading lh white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading lh pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial Loading lh annotations from /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading rh pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial Loading rh annotations from /space/freesurfer/subjects/test/bert.Darwin/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 /space/freesurfer/subjects/test/bert.Darwin/mri/ribbon.mgz Loading filled from /space/freesurfer/subjects/test/bert.Darwin/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8699 vertices from left hemi Ripped 8267 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 /space/freesurfer/subjects/test/bert.Darwin/mri/aseg.mgz Loading Ctx Seg File /space/freesurfer/subjects/test/bert.Darwin/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 979591 Used brute-force search on 273 voxels Fixing Parahip LH WM Found 14 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 1650.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 17.000000 11 k 1.000000 12 k 1.000000 13 k 9.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1848.000000 1 k 2.000000 2 k 1.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 6.000000 7 k 1.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz \n mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject bert.Darwin --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv \n $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject bert.Darwin --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman UseRobust 0 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /space/freesurfer/subjects/test/bert.Darwin/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Jan 27 23:04:48 EST 2016 \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA1_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA1_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4394 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA2_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA2_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 419 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8328 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA3a_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA3a_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4227 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA3b_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA3b_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 298 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6281 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA4a_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA4a_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 545 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6329 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA4p_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA4p_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 366 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4436 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA6_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA6_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 815 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14404 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA44_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA44_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 459 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4640 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA45_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA45_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 1273 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4695 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.V1_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.V1_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 1392 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6033 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.V2_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.V2_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 3138 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11252 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.MT_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.MT_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 133016 Number of reverse mapping hits = 418 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2436 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.entorhinal_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1345 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject bert.Darwin --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.perirhinal_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1241 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA1_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1078 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA2_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2156 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA3a_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1542 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA3b_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2109 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA4a_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 360 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2679 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA4p_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1653 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA6_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 299 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7334 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA44_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2161 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.BA45_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 516 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1667 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.V1_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 881 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4286 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.V2_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 1478 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4812 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.MT_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 594 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.entorhinal_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 497 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./lh.perirhinal_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 133016 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 466 mri_label2label: Done \n mris_label2annot --s bert.Darwin --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose \n Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/label cmdline mris_label2annot --s bert.Darwin --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman subject bert.Darwin hemi lh SUBJECTS_DIR /space/freesurfer/subjects/test ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /space/freesurfer/subjects/test/bert.Darwin/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 92471 unhit vertices Writing annot to /space/freesurfer/subjects/test/bert.Darwin/label/lh.BA_exvivo.annot \n mris_label2annot --s bert.Darwin --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose \n Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/label cmdline mris_label2annot --s bert.Darwin --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman subject bert.Darwin hemi lh SUBJECTS_DIR /space/freesurfer/subjects/test ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /space/freesurfer/subjects/test/bert.Darwin/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 109163 unhit vertices Writing annot to /space/freesurfer/subjects/test/bert.Darwin/label/lh.BA_exvivo.thresh.annot \n mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab bert.Darwin lh white \n computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 251085 Total vertex volume 247826 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 1062 569 1955 2.479 0.496 0.119 0.030 12 1.2 BA1_exvivo 3572 2339 5347 2.278 0.516 0.105 0.021 25 3.0 BA2_exvivo 952 639 948 1.914 0.391 0.126 0.025 7 0.9 BA3a_exvivo 2283 1502 3338 1.958 0.640 0.096 0.020 16 1.8 BA3b_exvivo 1879 1040 3668 2.968 0.596 0.088 0.023 13 1.8 BA4a_exvivo 1379 879 2397 2.865 0.648 0.086 0.020 6 1.2 BA4p_exvivo 7950 5262 19421 3.144 0.579 0.113 0.024 69 7.4 BA6_exvivo 2366 1624 5576 2.987 0.532 0.123 0.023 26 2.2 BA44_exvivo 3881 2610 7891 2.736 0.540 0.123 0.025 45 3.8 BA45_exvivo 3461 2232 3623 1.622 0.478 0.123 0.028 36 4.0 V1_exvivo 8794 5617 11683 1.987 0.540 0.141 0.036 118 12.8 V2_exvivo 1907 1265 3489 2.620 0.377 0.134 0.027 26 2.1 MT_exvivo 511 339 1156 2.844 0.925 0.133 0.031 5 0.7 perirhinal_exvivo 548 373 1263 2.969 0.658 0.083 0.015 3 0.3 entorhinal_exvivo \n mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab bert.Darwin lh white \n computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 251085 Total vertex volume 247826 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 641 330 1175 2.490 0.497 0.122 0.036 8 0.8 BA1_exvivo 1279 851 2134 2.303 0.473 0.088 0.017 6 0.8 BA2_exvivo 787 526 739 1.884 0.344 0.132 0.027 6 0.8 BA3a_exvivo 1397 930 1571 1.626 0.373 0.073 0.012 5 0.7 BA3b_exvivo 1924 1049 3636 3.002 0.636 0.083 0.024 13 1.9 BA4a_exvivo 1064 695 1746 2.702 0.611 0.087 0.020 5 0.9 BA4p_exvivo 4337 2796 10566 3.170 0.535 0.105 0.023 33 4.1 BA6_exvivo 1704 1182 4085 2.993 0.535 0.128 0.024 19 1.7 BA44_exvivo 1581 1074 3758 2.947 0.507 0.135 0.027 21 1.7 BA45_exvivo 3708 2365 3905 1.617 0.465 0.120 0.028 37 4.3 V1_exvivo 4420 2794 5346 1.879 0.520 0.146 0.039 64 7.2 V2_exvivo 467 301 937 2.868 0.429 0.136 0.022 6 0.4 MT_exvivo 237 159 675 2.959 0.920 0.097 0.018 2 0.2 perirhinal_exvivo 307 210 847 3.228 0.641 0.075 0.013 1 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Wed Jan 27 23:11:00 EST 2016 \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA1_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA1_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 286 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4248 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA2_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA2_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 474 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7161 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA3a_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA3a_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4132 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA3b_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA3b_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4869 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA4a_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA4a_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 507 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6254 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA4p_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA4p_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 287 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4760 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA6_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA6_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 880 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13136 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA44_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA44_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 1130 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8042 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA45_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA45_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 1487 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6842 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.V1_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.V1_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 1524 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6251 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.V2_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.V2_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 3209 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11225 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.MT_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.MT_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/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 131968 Number of reverse mapping hits = 408 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2340 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.entorhinal_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1101 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject bert.Darwin --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.perirhinal_exvivo.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 803 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA1_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 962 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA2_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2792 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA3a_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1733 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA3b_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2387 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA4a_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1549 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA4p_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1545 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA6_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7333 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA44_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1153 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.BA45_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 385 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1563 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.V1_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 939 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4171 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.V2_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 1374 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4811 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.MT_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 284 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.entorhinal_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 705 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /space/freesurfer/subjects/test/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject bert.Darwin --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface \n srclabel = /space/freesurfer/subjects/test/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert.Darwin trglabel = ./rh.perirhinal_exvivo.thresh.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 /space/freesurfer/subjects/test FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /space/freesurfer/subjects/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white Reading target registration /space/freesurfer/subjects/test/bert.Darwin/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 131968 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 299 mri_label2label: Done \n mris_label2annot --s bert.Darwin --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose \n Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/label cmdline mris_label2annot --s bert.Darwin --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman subject bert.Darwin hemi rh SUBJECTS_DIR /space/freesurfer/subjects/test ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /space/freesurfer/subjects/test/bert.Darwin/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 90539 unhit vertices Writing annot to /space/freesurfer/subjects/test/bert.Darwin/label/rh.BA_exvivo.annot \n mris_label2annot --s bert.Darwin --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose \n Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/bert.Darwin/label cmdline mris_label2annot --s bert.Darwin --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Darwin hostname gust.nmr.mgh.harvard.edu machine x86_64 user zkaufman subject bert.Darwin hemi rh SUBJECTS_DIR /space/freesurfer/subjects/test ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /space/freesurfer/subjects/test/bert.Darwin/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 109354 unhit vertices Writing annot to /space/freesurfer/subjects/test/bert.Darwin/label/rh.BA_exvivo.thresh.annot \n mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab bert.Darwin rh white \n computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 248640 Total vertex volume 244954 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 923 467 1737 2.562 0.512 0.117 0.027 11 1.0 BA1_exvivo 3359 2207 5274 2.354 0.504 0.099 0.019 23 2.6 BA2_exvivo 1043 688 977 1.919 0.417 0.122 0.028 8 1.2 BA3a_exvivo 2129 1322 2803 1.854 0.605 0.092 0.019 15 1.6 BA3b_exvivo 1745 973 3311 2.937 0.506 0.096 0.024 13 1.7 BA4a_exvivo 1165 777 2057 2.781 0.577 0.095 0.022 6 1.1 BA4p_exvivo 6882 4454 15717 3.002 0.624 0.112 0.025 67 7.5 BA6_exvivo 3721 2492 7726 2.901 0.468 0.105 0.019 27 2.7 BA44_exvivo 5106 3385 10748 2.750 0.524 0.127 0.027 60 5.6 BA45_exvivo 3880 2448 4471 1.766 0.528 0.116 0.030 36 4.6 V1_exvivo 8730 5708 12067 2.051 0.552 0.145 0.035 127 12.1 V2_exvivo 1958 1349 3382 2.623 0.436 0.120 0.023 18 1.7 MT_exvivo 451 317 1381 3.266 0.706 0.143 0.042 5 0.8 perirhinal_exvivo 337 233 793 2.875 0.510 0.083 0.013 1 0.2 entorhinal_exvivo \n mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab bert.Darwin rh white \n computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /space/freesurfer/subjects/test/bert.Darwin/mri/wm.mgz... reading input surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... reading input pial surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.pial... reading input white surface /space/freesurfer/subjects/test/bert.Darwin/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 248640 Total vertex volume 244954 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.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 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) lhCtxGM: 247391.649 247018.000 diff= 373.6 pctdiff= 0.151 rhCtxGM: 244958.069 245085.000 diff= -126.9 pctdiff=-0.052 lhCtxWM: 245711.757 246041.000 diff= -329.2 pctdiff=-0.134 rhCtxWM: 245178.936 245629.000 diff= -450.1 pctdiff=-0.184 SubCortGMVol 60440.000 SupraTentVol 1060577.411 (1059268.000) diff=1309.411 pctdiff=0.123 SupraTentVolNotVent 1045576.411 (1044267.000) diff=1309.411 pctdiff=0.125 BrainSegVol 1224529.000 (1221729.000) diff=2800.000 pctdiff=0.229 BrainSegVolNotVent 1205371.000 (1204557.411) diff=813.589 pctdiff=0.067 BrainSegVolNotVent 1205371.000 CerebellumVol 160823.000 VentChorVol 15001.000 3rd4th5thCSF 4157.000 CSFVol 1357.000, OptChiasmVol 281.000 MaskVol 1801939.000 680 320 1222 2.557 0.453 0.112 0.023 7 0.6 BA1_exvivo 1740 1150 2925 2.392 0.535 0.089 0.017 10 1.2 BA2_exvivo 937 600 812 1.933 0.424 0.123 0.027 7 1.1 BA3a_exvivo 1751 1117 2005 1.715 0.501 0.080 0.013 7 0.9 BA3b_exvivo 1107 594 1810 2.696 0.513 0.104 0.043 18 2.4 BA4a_exvivo 973 655 1694 2.798 0.652 0.098 0.025 5 1.1 BA4p_exvivo 4403 2825 9866 2.971 0.630 0.109 0.021 36 3.7 BA6_exvivo 914 607 2147 3.031 0.375 0.119 0.025 10 0.9 BA44_exvivo 1436 947 3469 2.880 0.446 0.128 0.027 19 1.5 BA45_exvivo 3681 2338 4151 1.758 0.523 0.115 0.028 32 4.3 V1_exvivo 4365 2791 5376 1.872 0.548 0.150 0.041 69 7.0 V2_exvivo 197 151 401 2.634 0.471 0.111 0.022 1 0.2 MT_exvivo 230 165 835 3.244 0.673 0.134 0.035 3 0.3 perirhinal_exvivo 200 141 607 3.215 0.525 0.087 0.014 1 0.1 entorhinal_exvivo #------------------------------------------ Started at Wed Jan 27 12:11:51 EST 2016 Ended at Wed Jan 27 23:16:56 EST 2016 #@#%# recon-all-run-time-hours 11.085 recon-all -s bert.Darwin finished without error at Wed Jan 27 23:16:56 EST 2016