Wed Jan 18 18:13:10 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert /usr/local/freesurfer/freesurfer/bin/recon-all -s bert -parallel -all subjid bert setenv SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux terrier 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 4096 memorylocked 64 kbytes maxproc 4096 total used free shared buffers cached Mem: 37012196 26344888 10667308 1420 988416 23633128 -/+ buffers/cache: 1723344 35288852 Swap: 8393924 37412 8356512 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:10-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/18-23:13:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: zkaufman Machine: terrier Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Jan 18 18:13:12 EST 2017 Found 3 runs /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert mri_robust_template --mov /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001-iscale.txt /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002-iscale.txt /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.lta /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.lta /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003.lta $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --mov: Using /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 '/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz'... converting source '/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.mgz'... converting source '/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003.mgz'... converting source '/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 ( /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/002.mgz ) to TP 1 ( /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz ) [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/003.mgz ) to TP 1 ( /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: - 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: /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 1 minutes and 11 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert mri_convert /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig.mgz --conform mri_convert.bin /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/transforms/talairach.xfm /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig.mgz /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jan 18 18:14:32 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri /usr/local/freesurfer/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux terrier 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed Jan 18 18:14:32 EST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.11068 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11068/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11068/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter 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.11068/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jan 18 18:14:35 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.11068/nu0.mnc ./tmp.mri_nu_correct.mni.11068/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11068/0/ -iterations 1000 -distance 50 [zkaufman@terrier:/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/] [2017-01-18 18:14:35] running: /usr/local/freesurfer/freesurfer/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.11068/0/ ./tmp.mri_nu_correct.mni.11068/nu0.mnc ./tmp.mri_nu_correct.mni.11068/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 mri_convert ./tmp.mri_nu_correct.mni.11068/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.11068/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.11068/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 18 18:15:28 EST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Wed Jan 18 18:15:28 EST 2017 Ended at Wed Jan 18 18:16:05 EST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Jan 18 18:16:07 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7584, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/freesurfer/bin/extract_talairach_avi_QA.awk /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/transforms/talairach_avi.log TalAviQA: 0.97388 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Jan 18 18:16:07 EST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri /usr/local/freesurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux terrier 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed Jan 18 18:16:07 EST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.12039 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12039/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.12039/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter 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.12039/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jan 18 18:16:09 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.12039/nu0.mnc ./tmp.mri_nu_correct.mni.12039/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12039/0/ [zkaufman@terrier:/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/] [2017-01-18 18:16:09] running: /usr/local/freesurfer/freesurfer/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.12039/0/ ./tmp.mri_nu_correct.mni.12039/nu0.mnc ./tmp.mri_nu_correct.mni.12039/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 -------------------------------------------------------- Iteration 2 Wed Jan 18 18:16:45 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.12039/nu1.mnc ./tmp.mri_nu_correct.mni.12039/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12039/1/ [zkaufman@terrier:/autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/] [2017-01-18 18:16:45] running: /usr/local/freesurfer/freesurfer/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.12039/1/ ./tmp.mri_nu_correct.mni.12039/nu1.mnc ./tmp.mri_nu_correct.mni.12039/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 mri_binarize --i ./tmp.mri_nu_correct.mni.12039/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12039/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.12039/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12039/ones.mgz sysname Linux hostname terrier machine x86_64 user zkaufman input ./tmp.mri_nu_correct.mni.12039/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.12039/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.12039/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12039/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12039/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12039/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12039/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12039/input.mean.dat sysname Linux hostname terrier machine x86_64 user zkaufman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12039/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.12039/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12039/ones.mgz --i ./tmp.mri_nu_correct.mni.12039/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12039/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12039/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12039/ones.mgz --i ./tmp.mri_nu_correct.mni.12039/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12039/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12039/output.mean.dat sysname Linux hostname terrier machine x86_64 user zkaufman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12039/ones.mgz Loading ./tmp.mri_nu_correct.mni.12039/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.12039/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.12039/nu2.mnc ./tmp.mri_nu_correct.mni.12039/nu2.mnc mul .96339522148081033593 Saving result to './tmp.mri_nu_correct.mni.12039/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.12039/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.12039/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.12039/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 7 seconds. mapping ( 8, 165) to ( 3, 110) Wed Jan 18 18:17:52 EST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed Jan 18 18:17:53 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE 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 110 white matter peak found at 110 gm peak at 81 (81), valley at 60 (60) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 58 (58) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 56 seconds. #-------------------------------------------- #@# Skull Stripping Wed Jan 18 18:19:50 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_em_register -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 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 = 108, using box (82,90,84) --> (120, 141,132) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 4.4 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.261 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.261423 @ (0.000, 0.000, 0.000) max log p = -4.261423 @ (0.000, 0.000, 0.000) max log p = -4.227329 @ (-2.273, -2.273, -6.818) max log p = -4.202916 @ (1.136, 3.409, 3.409) max log p = -4.187356 @ (0.568, -1.705, -0.568) max log p = -4.187356 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -0.6, -4.0): log p = -4.187 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.087, old_max_log_p =-4.187 (thresh=-4.2) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.06580 0.14032 -26.08343; 0.00000 -0.12074 0.91709 22.78377; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.087, old_max_log_p =-4.087 (thresh=-4.1) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.06580 0.14032 -26.08343; 0.00000 -0.12074 0.91709 22.78377; 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=-4.010, old_max_log_p =-4.087 (thresh=-4.1) 1.09389 -0.00454 0.02732 -16.49946; -0.00001 1.08052 0.17256 -29.72448; -0.03339 -0.14905 0.89509 30.10676; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.010, old_max_log_p =-4.010 (thresh=-4.0) 1.09389 -0.00454 0.02732 -16.49946; -0.00001 1.08052 0.17256 -29.72448; -0.03339 -0.14905 0.89509 30.10676; 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=-4.004, old_max_log_p =-4.010 (thresh=-4.0) 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03347 -0.14940 0.89719 29.91735; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.002, old_max_log_p =-4.004 (thresh=-4.0) 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.002 (old=-4.261) transform before final EM align: 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000 final transform: 1.09389 -0.00454 0.02732 -16.49946; -0.00000 1.07672 0.17195 -29.12062; -0.03355 -0.14975 0.89929 29.72749; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 927.395014 mri_em_register stimesec 1.139826 mri_em_register ru_maxrss 609812 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157369 mri_em_register ru_majflt 1 mri_em_register ru_nswap 0 mri_em_register ru_inblock 149440 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 597 mri_em_register ru_nivcsw 4545 registration took 4 minutes and 26 seconds. mri_watershed -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=116 z=117 r=86 first estimation of the main basin volume: 2758891 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=109, y=98, z=75, 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=9781326048 voxels, voxel volume =1.000 = 9781326048 mmm3 = 9781325.824 cm3 done. PostAnalyze...Basin Prior 100 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=10457 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=3, CSF_MAX=16 , nb = 43226 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=64 , nb = -1034155578 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=36 , nb = -1062238591 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=17 , nb = 1084178984 LEFT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=15 , nb = 1076067646 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1070674064 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 16, 32, 60, 81 after analyzing : 16, 50, 60, 57 RIGHT_CER before analyzing : 64, 66, 68, 92 after analyzing : 64, 67, 68, 73 LEFT_CER before analyzing : 36, 57, 70, 91 after analyzing : 36, 65, 70, 71 RIGHT_BRAIN before analyzing : 17, 34, 60, 81 after analyzing : 17, 51, 60, 58 LEFT_BRAIN before analyzing : 15, 31, 60, 80 after analyzing : 15, 50, 60, 57 OTHER before analyzing : 6, 8, 19, 40 after analyzing : 6, 19, 25, 24 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 = 71.523, std = 8.960 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.84, sigma = 4.29 after rotation: sse = 2.84, sigma = 4.29 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.87, its var is 3.55 before Erosion-Dilatation 0.23% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...49 iterations mri_strip_skull: done peeling brain Brain Size = 1809591 voxels, voxel volume = 1.000 mm3 = 1809591 mmm3 = 1809.591 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 26.620953 mri_watershed stimesec 0.404938 mri_watershed ru_maxrss 840468 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 217302 mri_watershed ru_majflt 5 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9048 mri_watershed ru_oublock 2784 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 10128 mri_watershed ru_nivcsw 280 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Jan 18 18:24:39 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_em_register -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (65, 59, 25) --> (191, 181, 206) using (107, 100, 116) as brain centroid... mean wm in atlas = 107, using box (92,85,94) --> (122, 114,138) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 4.0 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -3.845 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.844556 @ (0.000, 0.000, 0.000) max log p = -3.844556 @ (0.000, 0.000, 0.000) max log p = -3.800218 @ (-2.273, 2.273, -6.818) max log p = -3.766848 @ (-1.136, -1.136, 3.409) max log p = -3.756655 @ (-0.568, 0.568, 0.568) max log p = -3.753510 @ (0.852, -1.989, -0.284) Found translation: (-3.1, -0.3, -3.1): log p = -3.754 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.563, old_max_log_p =-3.754 (thresh=-3.7) 1.15000 0.00000 0.00000 -22.60431; 0.00000 1.06580 0.11927 -21.10135; 0.00000 -0.13053 0.84273 29.55746; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.563, old_max_log_p =-3.563 (thresh=-3.6) 1.15000 0.00000 0.00000 -22.60431; 0.00000 1.06580 0.11927 -21.10135; 0.00000 -0.13053 0.84273 29.55746; 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=-3.495, old_max_log_p =-3.563 (thresh=-3.6) 1.10569 0.02644 0.03375 -21.80483; -0.03620 1.01510 0.16659 -17.47288; -0.03622 -0.20734 0.86390 41.02398; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.492, old_max_log_p =-3.495 (thresh=-3.5) 1.12703 0.03383 0.00557 -22.36166; -0.03688 1.03413 0.16971 -20.03717; -0.00002 -0.20636 0.86454 36.19831; 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=-3.461, old_max_log_p =-3.492 (thresh=-3.5) 1.12555 0.03046 0.01970 -23.78675; -0.03670 1.03050 0.16911 -19.10137; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.459, old_max_log_p =-3.461 (thresh=-3.5) 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 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 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.459 (old=-3.845) transform before final EM align: 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 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 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 4.0 after pass:transform: ( 1.13, 0.03, 0.02, -23.79) ( -0.04, 1.03, 0.17, -18.94) ( -0.02, -0.21, 0.87, 39.51) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 823.352831 mri_em_register stimesec 1.090834 mri_em_register ru_maxrss 599032 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158636 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 799 mri_em_register ru_nivcsw 3937 registration took 4 minutes and 3 seconds. #-------------------------------------- #@# CA Normalize Wed Jan 18 18:28:42 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (65, 59, 25) --> (191, 181, 206) using (107, 100, 116) as brain centroid... mean wm in atlas = 107, using box (92,85,94) --> (122, 114,138) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 4.0 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.12555 0.03046 0.01970 -23.78675; -0.03666 1.02930 0.16892 -18.93919; -0.01848 -0.20713 0.86535 39.50742; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 57, 21) --> (187, 168, 209) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 7969 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 58, 19) --> (130, 166, 209) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 2 of 7639 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 144, 54) --> (171, 186, 115) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 144, 50) --> (128, 183, 115) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 23 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 132, 94) --> (143, 199, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 650 (0.0%) samples deleted using 16366 total control points for intensity normalization... bias field = 0.964 +- 0.045 161 of 16364 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 57, 21) --> (187, 168, 209) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 1 of 8286 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 58, 19) --> (130, 166, 209) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 3 of 7964 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 144, 54) --> (171, 186, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 39 of 144 (27.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 144, 50) --> (128, 183, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 66 (74.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 132, 94) --> (143, 199, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 136 of 701 (19.4%) samples deleted using 17161 total control points for intensity normalization... bias field = 1.032 +- 0.038 98 of 16860 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 57, 21) --> (187, 168, 209) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 4 of 8310 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 58, 19) --> (130, 166, 209) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 9 of 8043 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 144, 54) --> (171, 186, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 103 of 196 (52.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 144, 50) --> (128, 183, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 53 of 64 (82.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 132, 94) --> (143, 199, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 345 of 706 (48.9%) samples deleted using 17319 total control points for intensity normalization... bias field = 1.025 +- 0.033 70 of 16674 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 21 seconds. #-------------------------------------- #@# CA Reg Wed Jan 18 18:30:03 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_ca_register -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.04 (predicted orig area = 7.7) 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=0.894, neg=0, invalid=762 0001: dt=237.608081, rms=0.800 (10.532%), neg=0, invalid=762 0002: dt=221.952000, rms=0.766 (4.284%), neg=0, invalid=762 0003: dt=137.346032, rms=0.755 (1.486%), neg=0, invalid=762 0004: dt=295.936000, rms=0.746 (1.160%), neg=0, invalid=762 0005: dt=129.472000, rms=0.741 (0.693%), neg=0, invalid=762 0006: dt=295.936000, rms=0.737 (0.468%), neg=0, invalid=762 0007: dt=129.472000, rms=0.734 (0.369%), neg=0, invalid=762 0008: dt=295.936000, rms=0.732 (0.329%), neg=0, invalid=762 0009: dt=129.472000, rms=0.730 (0.229%), neg=0, invalid=762 0010: dt=129.472000, rms=0.729 (0.156%), neg=0, invalid=762 0011: dt=129.472000, rms=0.728 (0.240%), neg=0, invalid=762 0012: dt=129.472000, rms=0.725 (0.341%), neg=0, invalid=762 0013: dt=129.472000, rms=0.723 (0.315%), neg=0, invalid=762 0014: dt=129.472000, rms=0.720 (0.331%), neg=0, invalid=762 0015: dt=129.472000, rms=0.718 (0.280%), neg=0, invalid=762 0016: dt=129.472000, rms=0.717 (0.234%), neg=0, invalid=762 0017: dt=129.472000, rms=0.715 (0.209%), neg=0, invalid=762 0018: dt=129.472000, rms=0.714 (0.168%), neg=0, invalid=762 0019: dt=129.472000, rms=0.713 (0.136%), neg=0, invalid=762 0020: dt=129.472000, rms=0.712 (0.130%), neg=0, invalid=762 0021: dt=129.472000, rms=0.711 (0.158%), neg=0, invalid=762 0022: dt=129.472000, rms=0.710 (0.128%), neg=0, invalid=762 0023: dt=129.472000, rms=0.709 (0.097%), neg=0, invalid=762 0024: dt=129.472000, rms=0.709 (0.119%), neg=0, invalid=762 0025: dt=129.472000, rms=0.708 (0.124%), neg=0, invalid=762 0026: dt=129.472000, rms=0.707 (0.154%), neg=0, invalid=762 0027: dt=129.472000, rms=0.705 (0.155%), neg=0, invalid=762 0028: dt=129.472000, rms=0.704 (0.140%), neg=0, invalid=762 0029: dt=129.472000, rms=0.704 (0.106%), neg=0, invalid=762 0030: dt=129.472000, rms=0.703 (0.113%), neg=0, invalid=762 0031: dt=129.472000, rms=0.702 (0.141%), neg=0, invalid=762 0032: dt=129.472000, rms=0.701 (0.160%), neg=0, invalid=762 0033: dt=129.472000, rms=0.700 (0.150%), neg=0, invalid=762 0034: dt=129.472000, rms=0.699 (0.094%), neg=0, invalid=762 0035: dt=129.472000, rms=0.698 (0.098%), neg=0, invalid=762 0036: dt=129.472000, rms=0.697 (0.156%), neg=0, invalid=762 0037: dt=129.472000, rms=0.696 (0.132%), neg=0, invalid=762 0038: dt=129.472000, rms=0.696 (0.106%), neg=0, invalid=762 0039: dt=129.472000, rms=0.695 (0.087%), neg=0, invalid=762 0040: dt=517.888000, rms=0.694 (0.206%), neg=0, invalid=762 0041: dt=0.000000, rms=0.694 (0.002%), neg=0, invalid=762 0042: dt=0.850000, rms=0.694 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0043: dt=129.472000, rms=0.693 (0.278%), neg=0, invalid=762 0044: dt=517.888000, rms=0.691 (0.242%), neg=0, invalid=762 0045: dt=517.888000, rms=0.691 (-0.610%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.704, neg=0, invalid=762 0046: dt=90.871795, rms=0.698 (0.900%), neg=0, invalid=762 0047: dt=90.757946, rms=0.690 (1.103%), neg=0, invalid=762 0048: dt=41.111111, rms=0.687 (0.511%), neg=0, invalid=762 0049: dt=184.967033, rms=0.681 (0.861%), neg=0, invalid=762 0050: dt=36.213992, rms=0.676 (0.677%), neg=0, invalid=762 0051: dt=248.832000, rms=0.671 (0.753%), neg=0, invalid=762 0052: dt=31.104000, rms=0.667 (0.545%), neg=0, invalid=762 0053: dt=414.720000, rms=0.662 (0.800%), neg=0, invalid=762 0054: dt=58.880000, rms=0.659 (0.503%), neg=0, invalid=762 0055: dt=31.104000, rms=0.658 (0.135%), neg=0, invalid=762 0056: dt=31.104000, rms=0.657 (0.076%), neg=0, invalid=762 0057: dt=31.104000, rms=0.657 (0.117%), neg=0, invalid=762 0058: dt=31.104000, rms=0.656 (0.157%), neg=0, invalid=762 0059: dt=31.104000, rms=0.654 (0.171%), neg=0, invalid=762 0060: dt=31.104000, rms=0.653 (0.199%), neg=0, invalid=762 0061: dt=31.104000, rms=0.652 (0.221%), neg=0, invalid=762 0062: dt=31.104000, rms=0.650 (0.227%), neg=0, invalid=762 0063: dt=31.104000, rms=0.649 (0.226%), neg=0, invalid=762 0064: dt=31.104000, rms=0.647 (0.223%), neg=0, invalid=762 0065: dt=31.104000, rms=0.646 (0.224%), neg=0, invalid=762 0066: dt=31.104000, rms=0.644 (0.218%), neg=0, invalid=762 0067: dt=31.104000, rms=0.643 (0.216%), neg=0, invalid=762 0068: dt=31.104000, rms=0.642 (0.195%), neg=0, invalid=762 0069: dt=31.104000, rms=0.641 (0.173%), neg=0, invalid=762 0070: dt=31.104000, rms=0.640 (0.157%), neg=0, invalid=762 0071: dt=31.104000, rms=0.639 (0.131%), neg=0, invalid=762 0072: dt=31.104000, rms=0.638 (0.181%), neg=0, invalid=762 0073: dt=31.104000, rms=0.637 (0.152%), neg=0, invalid=762 0074: dt=31.104000, rms=0.636 (0.128%), neg=0, invalid=762 0075: dt=31.104000, rms=0.635 (0.114%), neg=0, invalid=762 0076: dt=31.104000, rms=0.635 (0.105%), neg=0, invalid=762 0077: dt=331.776000, rms=0.634 (0.096%), neg=0, invalid=762 0078: dt=165.888000, rms=0.634 (-0.514%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=762 0079: dt=88.888889, rms=0.632 (0.436%), neg=0, invalid=762 0080: dt=31.104000, rms=0.632 (0.034%), neg=0, invalid=762 0081: dt=31.104000, rms=0.632 (0.022%), neg=0, invalid=762 0082: dt=31.104000, rms=0.632 (0.024%), neg=0, invalid=762 0083: dt=31.104000, rms=0.631 (0.042%), neg=0, invalid=762 0084: dt=31.104000, rms=0.631 (0.043%), neg=0, invalid=762 0085: dt=31.104000, rms=0.631 (0.043%), neg=0, invalid=762 0086: dt=31.104000, rms=0.631 (0.037%), neg=0, invalid=762 0087: dt=124.416000, rms=0.630 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0088: dt=8.000000, rms=0.662 (0.217%), neg=0, invalid=762 0089: dt=2.800000, rms=0.662 (0.021%), neg=0, invalid=762 0090: dt=2.800000, rms=0.662 (0.006%), neg=0, invalid=762 0091: dt=2.800000, rms=0.662 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0092: dt=2.800000, rms=0.662 (0.142%), neg=0, invalid=762 0093: dt=2.000000, rms=0.662 (0.003%), neg=0, invalid=762 0094: dt=2.000000, rms=0.662 (0.000%), neg=0, invalid=762 0095: dt=2.000000, rms=0.662 (-0.013%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.740, neg=0, invalid=762 0096: dt=6.520179, rms=0.721 (2.586%), neg=0, invalid=762 0097: dt=8.398524, rms=0.716 (0.616%), neg=0, invalid=762 0098: dt=4.032000, rms=0.716 (0.052%), neg=0, invalid=762 0099: dt=4.032000, rms=0.716 (0.045%), neg=0, invalid=762 0100: dt=4.032000, rms=0.715 (0.030%), neg=0, invalid=762 0101: dt=4.032000, rms=0.715 (-0.068%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.716, neg=0, invalid=762 0102: dt=0.000000, rms=0.715 (0.097%), neg=0, invalid=762 0103: dt=0.000000, rms=0.715 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.768, neg=0, invalid=762 0104: dt=0.000000, rms=0.767 (0.085%), neg=0, invalid=762 0105: dt=0.000000, rms=0.767 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.768, neg=0, invalid=762 0106: dt=0.000000, rms=0.767 (0.085%), neg=0, invalid=762 0107: dt=0.000000, rms=0.767 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0108: dt=0.793722, rms=0.663 (2.331%), neg=0, invalid=762 0109: dt=0.080000, rms=0.663 (0.125%), neg=0, invalid=762 0110: dt=0.080000, rms=0.663 (-0.070%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0111: dt=0.028000, rms=0.663 (0.128%), neg=0, invalid=762 0112: dt=0.005000, rms=0.663 (-0.003%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.16653 (26) Left_Lateral_Ventricle (4): linear fit = 1.41 x + 0.0 (1529 voxels, overlap=0.299) Left_Lateral_Ventricle (4): linear fit = 1.41 x + 0.0 (1529 voxels, peak = 28), gca=28.3 gca peak = 0.15565 (16) mri peak = 0.18451 (30) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (1234 voxels, overlap=0.088) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1234 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.08371 (93) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1107 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1107 voxels, peak = 94), gca=93.6 gca peak = 0.20183 (93) mri peak = 0.06424 (96) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1044 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1044 voxels, peak = 95), gca=95.3 gca peak = 0.21683 (55) mri peak = 0.05052 (74) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1225 voxels, overlap=0.026) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1225 voxels, peak = 73), gca=73.4 gca peak = 0.30730 (58) mri peak = 0.06567 (76) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (1217 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (1217 voxels, peak = 75), gca=74.5 gca peak = 0.11430 (101) mri peak = 0.13335 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (83535 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (83535 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.13117 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (86868 voxels, overlap=0.510) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (86868 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.05343 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (38069 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (38069 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.05018 (80) Right_Cerebral_Cortex (42): linear fit = 1.38 x + 0.0 (39760 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.38 x + 0.0 (39760 voxels, peak = 80), gca=80.3 gca peak = 0.14161 (67) mri peak = 0.13270 (82) Right_Caudate (50): linear fit = 1.22 x + 0.0 (747 voxels, overlap=0.010) Right_Caudate (50): linear fit = 1.22 x + 0.0 (747 voxels, peak = 81), gca=81.4 gca peak = 0.15243 (71) mri peak = 0.11272 (79) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1202 voxels, overlap=0.462) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1202 voxels, peak = 76), gca=75.6 gca peak = 0.13336 (57) mri peak = 0.04211 (81) Left_Cerebellum_Cortex (8): linear fit = 1.45 x + 0.0 (20163 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.45 x + 0.0 (20163 voxels, peak = 82), gca=82.4 gca peak = 0.13252 (56) mri peak = 0.03616 (92) Right_Cerebellum_Cortex (47): linear fit = 1.59 x + 0.0 (24189 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.59 x + 0.0 (24189 voxels, peak = 89), gca=88.8 gca peak = 0.18181 (84) mri peak = 0.04557 (78) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10291 voxels, overlap=0.985) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10291 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.04513 (75) Right_Cerebellum_White_Matter (46): linear fit = 0.92 x + 0.0 (7778 voxels, overlap=0.881) Right_Cerebellum_White_Matter (46): linear fit = 0.92 x + 0.0 (7778 voxels, peak = 76), gca=75.9 gca peak = 0.21969 (57) mri peak = 0.09833 (77) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (608 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (608 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.08265 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (617 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (617 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.08658 (94) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6356 voxels, overlap=0.485) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6356 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.09352 (93) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5387 voxels, overlap=0.452) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5387 voxels, peak = 90), gca=90.1 gca peak = 0.13399 (79) mri peak = 0.07351 (88) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2896 voxels, overlap=0.389) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2896 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.07099 (88) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2917 voxels, overlap=0.662) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2917 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.14204 (87) Brain_Stem (16): linear fit = 1.11 x + 0.0 (11235 voxels, overlap=0.203) Brain_Stem (16): linear fit = 1.11 x + 0.0 (11235 voxels, peak = 88), gca=88.4 gca peak = 0.13281 (86) mri peak = 0.13466 (91) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1403 voxels, overlap=0.297) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1403 voxels, peak = 92), gca=92.5 gca peak = 0.12801 (89) mri peak = 0.10711 (94) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1616 voxels, overlap=0.535) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1616 voxels, peak = 94), gca=93.9 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.33355 (23) Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (911 voxels, overlap=0.237) Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (911 voxels, peak = 28), gca=28.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Cerebellum_Cortex = 0.13252 (56) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Right_Cerebellum_Cortex based on Left_Cerebellum_Cortex = 1.45 x + 0: 82 estimating mean gm scale to be 1.32 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.42 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0113: dt=88.580715, rms=0.648 (4.663%), neg=0, invalid=762 0114: dt=163.772926, rms=0.641 (1.005%), neg=0, invalid=762 0115: dt=517.888000, rms=0.630 (1.708%), neg=0, invalid=762 0116: dt=32.368000, rms=0.630 (0.055%), neg=0, invalid=762 0117: dt=55.488000, rms=0.630 (0.041%), neg=0, invalid=762 0118: dt=55.488000, rms=0.629 (0.061%), neg=0, invalid=762 0119: dt=55.488000, rms=0.629 (0.112%), neg=0, invalid=762 0120: dt=55.488000, rms=0.627 (0.179%), neg=0, invalid=762 0121: dt=55.488000, rms=0.626 (0.273%), neg=0, invalid=762 0122: dt=55.488000, rms=0.624 (0.353%), neg=0, invalid=762 0123: dt=55.488000, rms=0.621 (0.379%), neg=0, invalid=762 0124: dt=55.488000, rms=0.619 (0.328%), neg=0, invalid=762 0125: dt=55.488000, rms=0.617 (0.280%), neg=0, invalid=762 0126: dt=55.488000, rms=0.616 (0.183%), neg=0, invalid=762 0127: dt=55.488000, rms=0.616 (0.095%), neg=0, invalid=762 0128: dt=55.488000, rms=0.615 (0.068%), neg=0, invalid=762 0129: dt=55.488000, rms=0.615 (0.090%), neg=0, invalid=762 0130: dt=55.488000, rms=0.614 (0.125%), neg=0, invalid=762 0131: dt=55.488000, rms=0.613 (0.153%), neg=0, invalid=762 0132: dt=55.488000, rms=0.612 (0.138%), neg=0, invalid=762 0133: dt=55.488000, rms=0.611 (0.130%), neg=0, invalid=762 0134: dt=55.488000, rms=0.611 (0.100%), neg=0, invalid=762 0135: dt=55.488000, rms=0.610 (0.083%), neg=0, invalid=762 0136: dt=55.488000, rms=0.610 (0.075%), neg=0, invalid=762 0137: dt=55.488000, rms=0.609 (0.079%), neg=0, invalid=762 0138: dt=55.488000, rms=0.609 (0.089%), neg=0, invalid=762 0139: dt=55.488000, rms=0.608 (0.103%), neg=0, invalid=762 0140: dt=55.488000, rms=0.608 (0.097%), neg=0, invalid=762 0141: dt=55.488000, rms=0.607 (0.093%), neg=0, invalid=762 0142: dt=55.488000, rms=0.606 (0.082%), neg=0, invalid=762 0143: dt=55.488000, rms=0.606 (0.079%), neg=0, invalid=762 0144: dt=55.488000, rms=0.606 (0.075%), neg=0, invalid=762 0145: dt=55.488000, rms=0.605 (0.088%), neg=0, invalid=762 0146: dt=55.488000, rms=0.604 (0.098%), neg=0, invalid=762 0147: dt=55.488000, rms=0.604 (0.102%), neg=0, invalid=762 0148: dt=55.488000, rms=0.603 (0.096%), neg=0, invalid=762 0149: dt=55.488000, rms=0.603 (0.090%), neg=0, invalid=762 0150: dt=55.488000, rms=0.602 (0.086%), neg=0, invalid=762 0151: dt=55.488000, rms=0.602 (0.078%), neg=0, invalid=762 0152: dt=55.488000, rms=0.601 (0.071%), neg=0, invalid=762 0153: dt=55.488000, rms=0.601 (0.073%), neg=0, invalid=762 0154: dt=55.488000, rms=0.600 (0.072%), neg=0, invalid=762 0155: dt=55.488000, rms=0.600 (0.080%), neg=0, invalid=762 0156: dt=55.488000, rms=0.599 (0.080%), neg=0, invalid=762 0157: dt=55.488000, rms=0.599 (0.079%), neg=0, invalid=762 0158: dt=55.488000, rms=0.599 (0.064%), neg=0, invalid=762 0159: dt=55.488000, rms=0.598 (0.058%), neg=0, invalid=762 0160: dt=55.488000, rms=0.598 (0.053%), neg=0, invalid=762 0161: dt=55.488000, rms=0.598 (0.048%), neg=0, invalid=762 0162: dt=55.488000, rms=0.597 (0.049%), neg=0, invalid=762 0163: dt=55.488000, rms=0.597 (0.051%), neg=0, invalid=762 0164: dt=55.488000, rms=0.597 (0.050%), neg=0, invalid=762 0165: dt=55.488000, rms=0.596 (0.050%), neg=0, invalid=762 0166: dt=55.488000, rms=0.596 (0.046%), neg=0, invalid=762 0167: dt=55.488000, rms=0.596 (0.040%), neg=0, invalid=762 0168: dt=55.488000, rms=0.596 (0.034%), neg=0, invalid=762 0169: dt=55.488000, rms=0.596 (0.035%), neg=0, invalid=762 0170: dt=55.488000, rms=0.595 (0.032%), neg=0, invalid=762 0171: dt=55.488000, rms=0.595 (0.040%), neg=0, invalid=762 0172: dt=55.488000, rms=0.595 (0.040%), neg=0, invalid=762 0173: dt=55.488000, rms=0.595 (0.041%), neg=0, invalid=762 0174: dt=55.488000, rms=0.594 (0.034%), neg=0, invalid=762 0175: dt=55.488000, rms=0.594 (0.033%), neg=0, invalid=762 0176: dt=55.488000, rms=0.594 (0.031%), neg=0, invalid=762 0177: dt=55.488000, rms=0.594 (0.029%), neg=0, invalid=762 0178: dt=55.488000, rms=0.594 (0.029%), neg=0, invalid=762 0179: dt=55.488000, rms=0.594 (0.030%), neg=0, invalid=762 0180: dt=55.488000, rms=0.593 (0.032%), neg=0, invalid=762 0181: dt=55.488000, rms=0.593 (0.031%), neg=0, invalid=762 0182: dt=55.488000, rms=0.593 (0.030%), neg=0, invalid=762 0183: dt=55.488000, rms=0.593 (0.028%), neg=0, invalid=762 0184: dt=55.488000, rms=0.593 (0.026%), neg=0, invalid=762 0185: dt=55.488000, rms=0.592 (0.023%), neg=0, invalid=762 0186: dt=55.488000, rms=0.592 (0.021%), neg=0, invalid=762 0187: dt=2071.552000, rms=0.592 (0.064%), neg=0, invalid=762 0188: dt=110.976000, rms=0.592 (0.020%), neg=0, invalid=762 0189: dt=110.976000, rms=0.592 (0.004%), neg=0, invalid=762 0190: dt=110.976000, rms=0.592 (0.013%), neg=0, invalid=762 0191: dt=110.976000, rms=0.592 (0.016%), neg=0, invalid=762 0192: dt=110.976000, rms=0.592 (0.010%), neg=0, invalid=762 0193: dt=110.976000, rms=0.592 (0.008%), neg=0, invalid=762 0194: dt=517.888000, rms=0.591 (0.028%), neg=0, invalid=762 0195: dt=73.984000, rms=0.591 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=762 0196: dt=443.904000, rms=0.589 (0.405%), neg=0, invalid=762 0197: dt=32.368000, rms=0.589 (0.010%), neg=0, invalid=762 0198: dt=32.368000, rms=0.589 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 0199: dt=36.288000, rms=0.589 (0.218%), neg=0, invalid=762 0200: dt=145.152000, rms=0.586 (0.520%), neg=0, invalid=762 0201: dt=294.000000, rms=0.577 (1.564%), neg=0, invalid=762 0202: dt=35.692308, rms=0.574 (0.530%), neg=0, invalid=762 0203: dt=20.736000, rms=0.574 (0.019%), neg=0, invalid=762 0204: dt=20.736000, rms=0.574 (0.014%), neg=0, invalid=762 0205: dt=20.736000, rms=0.574 (0.014%), neg=0, invalid=762 0206: dt=20.736000, rms=0.574 (0.034%), neg=0, invalid=762 0207: dt=20.736000, rms=0.573 (0.110%), neg=0, invalid=762 0208: dt=20.736000, rms=0.572 (0.217%), neg=0, invalid=762 0209: dt=20.736000, rms=0.570 (0.307%), neg=0, invalid=762 0210: dt=20.736000, rms=0.569 (0.092%), neg=0, invalid=762 0211: dt=20.736000, rms=0.569 (0.147%), neg=0, invalid=762 0212: dt=20.736000, rms=0.568 (0.170%), neg=0, invalid=762 0213: dt=20.736000, rms=0.567 (0.174%), neg=0, invalid=762 0214: dt=20.736000, rms=0.567 (0.015%), neg=0, invalid=762 0215: dt=20.736000, rms=0.566 (0.021%), neg=0, invalid=762 0216: dt=10.368000, rms=0.566 (0.013%), neg=0, invalid=762 0217: dt=9.072000, rms=0.566 (0.011%), neg=0, invalid=762 0218: dt=1.134000, rms=0.566 (0.003%), neg=0, invalid=762 0219: dt=0.567000, rms=0.566 (0.001%), neg=0, invalid=762 0220: dt=0.035437, rms=0.566 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=762 0221: dt=145.152000, rms=0.562 (0.762%), neg=0, invalid=762 0222: dt=36.288000, rms=0.562 (0.059%), neg=0, invalid=762 0223: dt=145.152000, rms=0.561 (0.162%), neg=0, invalid=762 0224: dt=145.152000, rms=0.559 (0.346%), neg=0, invalid=762 0225: dt=36.288000, rms=0.559 (0.067%), neg=0, invalid=762 0226: dt=145.152000, rms=0.558 (0.092%), neg=0, invalid=762 0227: dt=124.416000, rms=0.557 (0.246%), neg=0, invalid=762 0228: dt=36.288000, rms=0.556 (0.072%), neg=0, invalid=762 0229: dt=145.152000, rms=0.556 (0.086%), neg=0, invalid=762 0230: dt=103.680000, rms=0.555 (0.166%), neg=0, invalid=762 0231: dt=36.288000, rms=0.555 (0.058%), neg=0, invalid=762 0232: dt=580.608000, rms=0.553 (0.378%), neg=0, invalid=762 0233: dt=82.944000, rms=0.551 (0.269%), neg=0, invalid=762 0234: dt=36.288000, rms=0.551 (0.031%), neg=0, invalid=762 0235: dt=36.288000, rms=0.551 (0.019%), neg=0, invalid=762 0236: dt=36.288000, rms=0.551 (0.034%), neg=0, invalid=762 0237: dt=36.288000, rms=0.550 (0.062%), neg=0, invalid=762 0238: dt=36.288000, rms=0.550 (0.099%), neg=0, invalid=762 0239: dt=36.288000, rms=0.549 (0.124%), neg=0, invalid=762 0240: dt=36.288000, rms=0.548 (0.126%), neg=0, invalid=762 0241: dt=36.288000, rms=0.548 (0.129%), neg=0, invalid=762 0242: dt=36.288000, rms=0.547 (0.124%), neg=0, invalid=762 0243: dt=36.288000, rms=0.546 (0.126%), neg=0, invalid=762 0244: dt=36.288000, rms=0.546 (0.136%), neg=0, invalid=762 0245: dt=36.288000, rms=0.545 (0.142%), neg=0, invalid=762 0246: dt=36.288000, rms=0.544 (0.145%), neg=0, invalid=762 0247: dt=36.288000, rms=0.543 (0.140%), neg=0, invalid=762 0248: dt=36.288000, rms=0.543 (0.135%), neg=0, invalid=762 0249: dt=36.288000, rms=0.542 (0.125%), neg=0, invalid=762 0250: dt=36.288000, rms=0.541 (0.117%), neg=0, invalid=762 0251: dt=36.288000, rms=0.541 (0.116%), neg=0, invalid=762 0252: dt=36.288000, rms=0.540 (0.120%), neg=0, invalid=762 0253: dt=36.288000, rms=0.539 (0.118%), neg=0, invalid=762 0254: dt=36.288000, rms=0.539 (0.111%), neg=0, invalid=762 0255: dt=36.288000, rms=0.538 (0.107%), neg=0, invalid=762 0256: dt=36.288000, rms=0.538 (0.101%), neg=0, invalid=762 0257: dt=36.288000, rms=0.537 (0.093%), neg=0, invalid=762 0258: dt=36.288000, rms=0.537 (0.091%), neg=0, invalid=762 0259: dt=36.288000, rms=0.536 (0.096%), neg=0, invalid=762 0260: dt=36.288000, rms=0.536 (0.094%), neg=0, invalid=762 0261: dt=36.288000, rms=0.535 (0.085%), neg=0, invalid=762 0262: dt=36.288000, rms=0.535 (0.079%), neg=0, invalid=762 0263: dt=36.288000, rms=0.534 (0.079%), neg=0, invalid=762 0264: dt=36.288000, rms=0.534 (0.075%), neg=0, invalid=762 0265: dt=36.288000, rms=0.534 (0.076%), neg=0, invalid=762 0266: dt=36.288000, rms=0.533 (0.072%), neg=0, invalid=762 0267: dt=36.288000, rms=0.533 (0.069%), neg=0, invalid=762 0268: dt=36.288000, rms=0.532 (0.061%), neg=0, invalid=762 0269: dt=36.288000, rms=0.532 (0.061%), neg=0, invalid=762 0270: dt=36.288000, rms=0.532 (0.060%), neg=0, invalid=762 0271: dt=36.288000, rms=0.531 (0.063%), neg=0, invalid=762 0272: dt=36.288000, rms=0.531 (0.065%), neg=0, invalid=762 0273: dt=36.288000, rms=0.531 (0.059%), neg=0, invalid=762 0274: dt=36.288000, rms=0.530 (0.057%), neg=0, invalid=762 0275: dt=36.288000, rms=0.530 (0.052%), neg=0, invalid=762 0276: dt=36.288000, rms=0.530 (0.042%), neg=0, invalid=762 0277: dt=36.288000, rms=0.530 (0.050%), neg=0, invalid=762 0278: dt=36.288000, rms=0.529 (0.044%), neg=0, invalid=762 0279: dt=36.288000, rms=0.529 (0.045%), neg=0, invalid=762 0280: dt=36.288000, rms=0.529 (0.046%), neg=0, invalid=762 0281: dt=36.288000, rms=0.529 (0.042%), neg=0, invalid=762 0282: dt=36.288000, rms=0.529 (0.044%), neg=0, invalid=762 0283: dt=36.288000, rms=0.528 (0.043%), neg=0, invalid=762 0284: dt=36.288000, rms=0.528 (0.040%), neg=0, invalid=762 0285: dt=36.288000, rms=0.528 (0.041%), neg=0, invalid=762 0286: dt=36.288000, rms=0.528 (0.041%), neg=0, invalid=762 0287: dt=36.288000, rms=0.527 (0.038%), neg=0, invalid=762 0288: dt=36.288000, rms=0.527 (0.037%), neg=0, invalid=762 0289: dt=36.288000, rms=0.527 (0.038%), neg=0, invalid=762 0290: dt=36.288000, rms=0.527 (0.035%), neg=0, invalid=762 0291: dt=36.288000, rms=0.527 (0.034%), neg=0, invalid=762 0292: dt=36.288000, rms=0.527 (0.034%), neg=0, invalid=762 0293: dt=36.288000, rms=0.526 (0.039%), neg=0, invalid=762 0294: dt=36.288000, rms=0.526 (0.036%), neg=0, invalid=762 0295: dt=36.288000, rms=0.526 (0.030%), neg=0, invalid=762 0296: dt=36.288000, rms=0.526 (0.030%), neg=0, invalid=762 0297: dt=36.288000, rms=0.526 (0.024%), neg=0, invalid=762 0298: dt=36.288000, rms=0.526 (0.033%), neg=0, invalid=762 0299: dt=36.288000, rms=0.525 (0.029%), neg=0, invalid=762 0300: dt=36.288000, rms=0.525 (0.028%), neg=0, invalid=762 0301: dt=36.288000, rms=0.525 (0.030%), neg=0, invalid=762 0302: dt=36.288000, rms=0.525 (0.026%), neg=0, invalid=762 0303: dt=36.288000, rms=0.525 (0.028%), neg=0, invalid=762 0304: dt=36.288000, rms=0.525 (0.027%), neg=0, invalid=762 0305: dt=36.288000, rms=0.525 (0.022%), neg=0, invalid=762 0306: dt=36.288000, rms=0.524 (0.025%), neg=0, invalid=762 0307: dt=36.288000, rms=0.524 (0.025%), neg=0, invalid=762 0308: dt=36.288000, rms=0.524 (0.025%), neg=0, invalid=762 0309: dt=36.288000, rms=0.524 (0.025%), neg=0, invalid=762 0310: dt=36.288000, rms=0.524 (0.026%), neg=0, invalid=762 0311: dt=36.288000, rms=0.524 (0.021%), neg=0, invalid=762 0312: dt=36.288000, rms=0.524 (0.022%), neg=0, invalid=762 0313: dt=36.288000, rms=0.524 (0.020%), neg=0, invalid=762 0314: dt=124.416000, rms=0.523 (0.014%), neg=0, invalid=762 0315: dt=124.416000, rms=0.523 (-0.035%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0316: dt=11.200000, rms=0.532 (0.143%), neg=0, invalid=762 0317: dt=25.600000, rms=0.531 (0.118%), neg=0, invalid=762 0318: dt=44.800000, rms=0.529 (0.295%), neg=0, invalid=762 0319: dt=128.000000, rms=0.527 (0.477%), neg=0, invalid=762 0320: dt=44.800000, rms=0.524 (0.523%), neg=0, invalid=762 0321: dt=32.000000, rms=0.523 (0.139%), neg=0, invalid=762 0322: dt=128.000000, rms=0.521 (0.473%), neg=0, invalid=762 0323: dt=24.810127, rms=0.520 (0.177%), neg=0, invalid=762 0324: dt=44.800000, rms=0.519 (0.208%), neg=0, invalid=762 0325: dt=44.800000, rms=0.518 (0.136%), neg=0, invalid=762 0326: dt=44.800000, rms=0.517 (0.145%), neg=0, invalid=762 0327: dt=38.400000, rms=0.517 (0.101%), neg=0, invalid=762 0328: dt=44.800000, rms=0.516 (0.117%), neg=0, invalid=762 0329: dt=32.000000, rms=0.516 (0.103%), neg=0, invalid=762 0330: dt=38.400000, rms=0.515 (0.061%), neg=0, invalid=762 0331: dt=38.400000, rms=0.515 (0.107%), neg=0, invalid=762 0332: dt=32.000000, rms=0.515 (0.067%), neg=0, invalid=762 0333: dt=44.800000, rms=0.514 (0.117%), neg=0, invalid=762 0334: dt=25.600000, rms=0.514 (0.036%), neg=0, invalid=762 0335: dt=25.600000, rms=0.513 (0.069%), neg=0, invalid=762 0336: dt=25.600000, rms=0.513 (0.095%), neg=0, invalid=762 0337: dt=25.600000, rms=0.512 (0.123%), neg=0, invalid=762 0338: dt=25.600000, rms=0.512 (0.137%), neg=0, invalid=762 0339: dt=25.600000, rms=0.511 (0.061%), neg=0, invalid=762 0340: dt=25.600000, rms=0.511 (0.068%), neg=0, invalid=762 0341: dt=25.600000, rms=0.510 (0.091%), neg=0, invalid=762 0342: dt=12.800000, rms=0.510 (0.014%), neg=0, invalid=762 0343: dt=3.200000, rms=0.510 (0.009%), neg=0, invalid=762 0344: dt=0.700000, rms=0.510 (0.001%), neg=0, invalid=762 0345: dt=0.700000, rms=0.510 (0.001%), neg=0, invalid=762 0346: dt=0.350000, rms=0.510 (0.001%), neg=0, invalid=762 0347: dt=0.175000, rms=0.510 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0348: dt=86.588235, rms=0.507 (0.771%), neg=0, invalid=762 0349: dt=11.200000, rms=0.506 (0.113%), neg=0, invalid=762 0350: dt=11.200000, rms=0.506 (0.043%), neg=0, invalid=762 0351: dt=11.200000, rms=0.506 (0.023%), neg=0, invalid=762 0352: dt=11.200000, rms=0.506 (0.025%), neg=0, invalid=762 0353: dt=11.200000, rms=0.505 (0.024%), neg=0, invalid=762 0354: dt=11.200000, rms=0.505 (0.048%), neg=0, invalid=762 0355: dt=11.200000, rms=0.505 (0.089%), neg=0, invalid=762 0356: dt=11.200000, rms=0.504 (0.118%), neg=0, invalid=762 0357: dt=11.200000, rms=0.504 (0.119%), neg=0, invalid=762 0358: dt=11.200000, rms=0.503 (0.099%), neg=0, invalid=762 0359: dt=11.200000, rms=0.503 (0.075%), neg=0, invalid=762 0360: dt=11.200000, rms=0.502 (0.055%), neg=0, invalid=762 0361: dt=11.200000, rms=0.502 (0.052%), neg=0, invalid=762 0362: dt=11.200000, rms=0.502 (0.057%), neg=0, invalid=762 0363: dt=11.200000, rms=0.502 (0.072%), neg=0, invalid=762 0364: dt=11.200000, rms=0.501 (0.087%), neg=0, invalid=762 0365: dt=11.200000, rms=0.501 (0.101%), neg=0, invalid=762 0366: dt=11.200000, rms=0.500 (0.101%), neg=0, invalid=762 0367: dt=11.200000, rms=0.500 (0.098%), neg=0, invalid=762 0368: dt=11.200000, rms=0.499 (0.090%), neg=0, invalid=762 0369: dt=11.200000, rms=0.499 (0.085%), neg=0, invalid=762 0370: dt=11.200000, rms=0.498 (0.083%), neg=0, invalid=762 0371: dt=11.200000, rms=0.498 (0.076%), neg=0, invalid=762 0372: dt=11.200000, rms=0.498 (0.082%), neg=0, invalid=762 0373: dt=11.200000, rms=0.497 (0.074%), neg=0, invalid=762 0374: dt=11.200000, rms=0.497 (0.071%), neg=0, invalid=762 0375: dt=11.200000, rms=0.497 (0.062%), neg=0, invalid=762 0376: dt=11.200000, rms=0.496 (0.047%), neg=0, invalid=762 0377: dt=11.200000, rms=0.496 (0.056%), neg=0, invalid=762 0378: dt=11.200000, rms=0.496 (0.045%), neg=0, invalid=762 0379: dt=11.200000, rms=0.496 (0.049%), neg=0, invalid=762 0380: dt=11.200000, rms=0.495 (0.046%), neg=0, invalid=762 0381: dt=11.200000, rms=0.495 (0.045%), neg=0, invalid=762 0382: dt=11.200000, rms=0.495 (0.042%), neg=0, invalid=762 0383: dt=11.200000, rms=0.495 (0.034%), neg=0, invalid=762 0384: dt=11.200000, rms=0.495 (0.028%), neg=0, invalid=762 0385: dt=11.200000, rms=0.494 (0.033%), neg=0, invalid=762 0386: dt=11.200000, rms=0.494 (0.029%), neg=0, invalid=762 0387: dt=11.200000, rms=0.494 (0.031%), neg=0, invalid=762 0388: dt=11.200000, rms=0.494 (0.040%), neg=0, invalid=762 0389: dt=11.200000, rms=0.494 (0.038%), neg=0, invalid=762 0390: dt=11.200000, rms=0.494 (0.039%), neg=0, invalid=762 0391: dt=11.200000, rms=0.493 (0.030%), neg=0, invalid=762 0392: dt=11.200000, rms=0.493 (0.029%), neg=0, invalid=762 0393: dt=11.200000, rms=0.493 (0.030%), neg=0, invalid=762 0394: dt=11.200000, rms=0.493 (0.030%), neg=0, invalid=762 0395: dt=11.200000, rms=0.493 (0.025%), neg=0, invalid=762 0396: dt=11.200000, rms=0.493 (0.023%), neg=0, invalid=762 0397: dt=11.200000, rms=0.493 (0.025%), neg=0, invalid=762 0398: dt=11.200000, rms=0.492 (0.023%), neg=0, invalid=762 0399: dt=44.800000, rms=0.492 (0.010%), neg=0, invalid=762 0400: dt=44.800000, rms=0.492 (-0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.512, neg=0, invalid=762 0401: dt=0.000000, rms=0.512 (0.042%), neg=0, invalid=762 0402: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=762 0403: dt=0.000000, rms=0.512 (0.042%), neg=0, invalid=762 0404: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.551, neg=0, invalid=762 0405: dt=1.536000, rms=0.547 (0.667%), neg=0, invalid=762 0406: dt=0.112000, rms=0.547 (0.005%), neg=0, invalid=762 0407: dt=0.112000, rms=0.547 (0.001%), neg=0, invalid=762 0408: dt=0.112000, rms=0.547 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.547, neg=0, invalid=762 0409: dt=0.768000, rms=0.547 (0.135%), neg=0, invalid=762 0410: dt=0.320000, rms=0.547 (0.009%), neg=0, invalid=762 0411: dt=0.320000, rms=0.547 (-0.004%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.503, neg=0, invalid=762 0412: dt=0.448000, rms=0.491 (2.463%), neg=0, invalid=762 0413: dt=1.280000, rms=0.484 (1.430%), neg=0, invalid=762 0414: dt=0.000000, rms=0.484 (-0.000%), neg=0, invalid=762 0415: dt=0.050000, rms=0.484 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0416: dt=0.448000, rms=0.480 (0.754%), neg=0, invalid=762 0417: dt=0.448000, rms=0.480 (0.120%), neg=0, invalid=762 0418: dt=0.448000, rms=0.479 (0.091%), neg=0, invalid=762 0419: dt=0.448000, rms=0.479 (0.056%), neg=0, invalid=762 0420: dt=0.448000, rms=0.479 (0.045%), neg=0, invalid=762 0421: dt=0.448000, rms=0.479 (0.041%), neg=0, invalid=762 0422: dt=0.448000, rms=0.478 (0.064%), neg=0, invalid=762 0423: dt=0.448000, rms=0.478 (0.088%), neg=0, invalid=762 0424: dt=0.448000, rms=0.477 (0.092%), neg=0, invalid=762 0425: dt=0.448000, rms=0.477 (0.085%), neg=0, invalid=762 0426: dt=0.448000, rms=0.477 (0.071%), neg=0, invalid=762 0427: dt=0.448000, rms=0.476 (0.056%), neg=0, invalid=762 0428: dt=0.448000, rms=0.476 (0.037%), neg=0, invalid=762 0429: dt=0.448000, rms=0.476 (0.019%), neg=0, invalid=762 0430: dt=0.448000, rms=0.476 (0.013%), neg=0, invalid=762 0431: dt=0.024000, rms=0.476 (-0.002%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0432: dt=0.000000, rms=0.474 (0.063%), neg=0, invalid=762 0433: dt=0.000000, rms=0.474 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0434: dt=23.120000, rms=0.474 (0.064%), neg=0, invalid=762 0435: dt=73.984000, rms=0.474 (0.004%), neg=0, invalid=762 0436: dt=73.984000, rms=0.474 (0.010%), neg=0, invalid=762 0437: dt=73.984000, rms=0.474 (0.020%), neg=0, invalid=762 0438: dt=73.984000, rms=0.474 (0.018%), neg=0, invalid=762 0439: dt=73.984000, rms=0.474 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0440: dt=1.944000, rms=0.474 (0.066%), neg=0, invalid=762 0441: dt=0.972000, rms=0.474 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0442: dt=145.152000, rms=0.472 (0.420%), neg=0, invalid=762 0443: dt=36.288000, rms=0.472 (0.047%), neg=0, invalid=762 0444: dt=36.288000, rms=0.472 (0.048%), neg=0, invalid=762 0445: dt=36.288000, rms=0.471 (0.072%), neg=0, invalid=762 0446: dt=36.288000, rms=0.471 (0.101%), neg=0, invalid=762 0447: dt=36.288000, rms=0.470 (0.113%), neg=0, invalid=762 0448: dt=36.288000, rms=0.470 (0.111%), neg=0, invalid=762 0449: dt=36.288000, rms=0.469 (0.113%), neg=0, invalid=762 0450: dt=36.288000, rms=0.469 (0.088%), neg=0, invalid=762 0451: dt=36.288000, rms=0.469 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0452: dt=23.172414, rms=0.468 (0.239%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0453: dt=44.800000, rms=0.467 (0.295%), neg=0, invalid=762 0454: dt=44.800000, rms=0.466 (0.205%), neg=0, invalid=762 0455: dt=44.800000, rms=0.465 (0.204%), neg=0, invalid=762 0456: dt=44.800000, rms=0.463 (0.325%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0457: dt=44.800000, rms=0.463 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 0458: dt=44.800000, rms=0.461 (0.319%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0459: dt=44.800000, rms=0.460 (0.201%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0460: dt=44.800000, rms=0.459 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0461: dt=44.800000, rms=0.459 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0462: dt=44.800000, rms=0.458 (0.226%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0463: dt=44.800000, rms=0.458 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 0464: dt=44.800000, rms=0.457 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0465: dt=44.800000, rms=0.457 (0.041%), neg=0, invalid=762 0466: dt=38.400000, rms=0.456 (0.198%), neg=0, invalid=762 0467: dt=11.200000, rms=0.456 (0.024%), neg=0, invalid=762 0468: dt=11.200000, rms=0.456 (0.026%), neg=0, invalid=762 0469: dt=11.200000, rms=0.456 (0.020%), neg=0, invalid=762 0470: dt=11.200000, rms=0.456 (0.026%), neg=0, invalid=762 0471: dt=11.200000, rms=0.455 (0.031%), neg=0, invalid=762 0472: dt=11.200000, rms=0.455 (0.036%), neg=0, invalid=762 0473: dt=11.200000, rms=0.455 (0.034%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0474: dt=80.747664, rms=0.451 (1.008%), neg=0, invalid=762 0475: dt=22.581940, rms=0.450 (0.235%), neg=0, invalid=762 0476: dt=22.581940, rms=0.449 (0.099%), neg=0, invalid=762 0477: dt=22.581940, rms=0.449 (0.108%), neg=0, invalid=762 0478: dt=22.581940, rms=0.448 (0.089%), neg=0, invalid=762 0479: dt=22.581940, rms=0.448 (0.085%), neg=0, invalid=762 0480: dt=44.800000, rms=0.448 (0.105%), neg=0, invalid=762 0481: dt=11.200000, rms=0.447 (0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0482: dt=2.560000, rms=0.455 (0.090%), neg=0, invalid=762 0483: dt=0.720000, rms=0.455 (0.004%), neg=0, invalid=762 0484: dt=0.720000, rms=0.455 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0485: dt=8.766284, rms=0.454 (0.295%), neg=0, invalid=762 0486: dt=10.232558, rms=0.453 (0.121%), neg=0, invalid=762 0487: dt=10.232558, rms=0.453 (0.115%), neg=0, invalid=762 0488: dt=10.232558, rms=0.452 (0.086%), neg=0, invalid=762 0489: dt=10.232558, rms=0.452 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0490: dt=57.295238, rms=0.448 (0.899%), neg=0, invalid=762 0491: dt=8.533333, rms=0.448 (0.062%), neg=0, invalid=762 0492: dt=8.533333, rms=0.448 (0.020%), neg=0, invalid=762 0493: dt=8.533333, rms=0.448 (-0.132%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0494: dt=0.000000, rms=0.453 (0.052%), neg=0, invalid=762 0495: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0496: dt=0.000000, rms=0.453 (0.052%), neg=0, invalid=762 0497: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=762 iter 0, gcam->neg = 481 after 12 iterations, nbhd size=1, neg = 0 0498: dt=1.930233, rms=0.423 (4.854%), neg=0, invalid=762 0499: dt=0.028000, rms=0.423 (0.021%), neg=0, invalid=762 0500: dt=0.028000, rms=0.423 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=762 0501: dt=0.080000, rms=0.423 (0.114%), neg=0, invalid=762 0502: dt=0.001750, rms=0.423 (-0.009%), neg=0, invalid=762 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 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0503: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0504: dt=27.744000, rms=0.411 (0.001%), neg=0, invalid=762 0505: dt=8.092000, rms=0.411 (0.000%), neg=0, invalid=762 0506: dt=8.092000, rms=0.411 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0507: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0508: dt=82.944000, rms=0.411 (0.046%), neg=0, invalid=762 0509: dt=145.152000, rms=0.411 (0.070%), neg=0, invalid=762 0510: dt=36.288000, rms=0.411 (0.015%), neg=0, invalid=762 0511: dt=36.288000, rms=0.411 (0.009%), neg=0, invalid=762 0512: dt=36.288000, rms=0.411 (0.016%), neg=0, invalid=762 0513: dt=36.288000, rms=0.410 (0.022%), neg=0, invalid=762 0514: dt=36.288000, rms=0.410 (0.026%), neg=0, invalid=762 0515: dt=36.288000, rms=0.410 (0.026%), neg=0, invalid=762 0516: dt=36.288000, rms=0.410 (0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0517: dt=2.800000, rms=0.411 (0.010%), neg=0, invalid=762 0518: dt=2.800000, rms=0.411 (0.004%), neg=0, invalid=762 0519: dt=2.800000, rms=0.411 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0520: dt=122.434783, rms=0.408 (0.700%), neg=0, invalid=762 0521: dt=24.847059, rms=0.407 (0.171%), neg=0, invalid=762 0522: dt=24.847059, rms=0.407 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0523: dt=24.847059, rms=0.406 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0524: dt=24.847059, rms=0.406 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0525: dt=24.847059, rms=0.406 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0526: dt=24.847059, rms=0.405 (0.145%), neg=0, invalid=762 0527: dt=24.847059, rms=0.404 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0528: dt=24.847059, rms=0.404 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0529: dt=24.847059, rms=0.404 (0.101%), neg=0, invalid=762 0530: dt=32.000000, rms=0.404 (0.005%), neg=0, invalid=762 0531: dt=32.000000, rms=0.403 (0.012%), neg=0, invalid=762 0532: dt=32.000000, rms=0.403 (0.015%), neg=0, invalid=762 0533: dt=32.000000, rms=0.403 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0534: dt=32.000000, rms=0.403 (0.023%), neg=0, invalid=762 0535: dt=32.000000, rms=0.403 (0.033%), neg=0, invalid=762 0536: dt=32.000000, rms=0.403 (0.037%), neg=0, invalid=762 0537: dt=32.000000, rms=0.403 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0538: dt=32.000000, rms=0.403 (0.041%), neg=0, invalid=762 0539: dt=32.000000, rms=0.402 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0540: dt=32.000000, rms=0.402 (0.054%), neg=0, invalid=762 0541: dt=32.000000, rms=0.402 (0.054%), neg=0, invalid=762 0542: dt=32.000000, rms=0.402 (0.051%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.406, neg=0, invalid=762 0543: dt=0.000000, rms=0.406 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=762 0544: dt=4.032000, rms=0.406 (0.026%), neg=0, invalid=762 0545: dt=4.032000, rms=0.405 (0.011%), neg=0, invalid=762 0546: dt=4.032000, rms=0.405 (0.006%), neg=0, invalid=762 0547: dt=4.032000, rms=0.405 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0548: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0549: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 iter 0, gcam->neg = 373 after 15 iterations, nbhd size=1, neg = 0 0550: dt=1.192045, rms=0.394 (1.729%), neg=0, invalid=762 0551: dt=0.000023, rms=0.394 (0.000%), neg=0, invalid=762 0552: dt=0.000023, rms=0.394 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 0553: dt=0.112000, rms=0.394 (0.064%), neg=0, invalid=762 0554: dt=0.112000, rms=0.394 (0.026%), neg=0, invalid=762 0555: dt=0.112000, rms=0.394 (0.018%), neg=0, invalid=762 0556: dt=0.112000, rms=0.394 (-0.020%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 12 minutes and 27 seconds. mri_ca_register utimesec 9455.193592 mri_ca_register stimesec 9.447563 mri_ca_register ru_maxrss 1333812 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 6386261 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63272 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 15060 mri_ca_register ru_nivcsw 20597 FSRUNTIME@ mri_ca_register 2.2074 hours 4 threads #-------------------------------------- #@# SubCort Seg Wed Jan 18 20:42:30 EST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname terrier machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects cd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 4 == 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/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.67 Atlas used for the 3D morph was /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.18979 (27) Left_Lateral_Ventricle (4): linear fit = 1.41 x + 0.0 (1310 voxels, overlap=0.179) Left_Lateral_Ventricle (4): linear fit = 1.41 x + 0.0 (1310 voxels, peak = 28), gca=28.3 gca peak = 0.17677 (13) mri peak = 0.16488 (30) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (1125 voxels, overlap=0.103) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1125 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.13060 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (803 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (803 voxels, peak = 95), gca=94.5 gca peak = 0.16930 (96) mri peak = 0.16726 (99) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (696 voxels, overlap=0.982) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (696 voxels, peak = 98), gca=98.4 gca peak = 0.24553 (55) mri peak = 0.08333 (72) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1173 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1173 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.09099 (77) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1128 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1128 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.15523 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (51442 voxels, overlap=0.595) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (51442 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.15966 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51860 voxels, overlap=0.517) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51860 voxels, peak = 105), gca=104.5 gca peak = 0.09712 (58) mri peak = 0.05527 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (40973 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (40973 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.05718 (80) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (39331 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (39331 voxels, peak = 78), gca=78.0 gca peak = 0.30970 (66) mri peak = 0.15706 (82) Right_Caudate (50): linear fit = 1.21 x + 0.0 (885 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.21 x + 0.0 (885 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.17139 (79) Left_Caudate (11): linear fit = 1.10 x + 0.0 (846 voxels, overlap=0.503) Left_Caudate (11): linear fit = 1.10 x + 0.0 (846 voxels, peak = 76), gca=75.6 gca peak = 0.13902 (56) mri peak = 0.06590 (79) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (29863 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (29863 voxels, peak = 79), gca=78.7 gca peak = 0.14777 (55) mri peak = 0.05989 (77) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (31677 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (31677 voxels, peak = 76), gca=76.2 gca peak = 0.16765 (84) mri peak = 0.13953 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (7461 voxels, overlap=0.237) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (7461 voxels, peak = 92), gca=92.0 gca peak = 0.18739 (84) mri peak = 0.09302 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6303 voxels, overlap=0.743) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6303 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.10071 (74) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (568 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (568 voxels, peak = 74), gca=74.4 gca peak = 0.33601 (57) mri peak = 0.12414 (79) Right_Amygdala (54): linear fit = 1.35 x + 0.0 (503 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.35 x + 0.0 (503 voxels, peak = 77), gca=76.7 gca peak = 0.11131 (90) mri peak = 0.09803 (92) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5113 voxels, overlap=0.787) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5113 voxels, peak = 94), gca=94.0 gca peak = 0.11793 (83) mri peak = 0.10817 (92) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (5156 voxels, overlap=0.447) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (5156 voxels, peak = 92), gca=91.7 gca peak = 0.08324 (81) mri peak = 0.07780 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2273 voxels, overlap=0.568) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2273 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.08811 (88) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1952 voxels, overlap=0.633) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1952 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.10941 (87) Brain_Stem (16): linear fit = 1.08 x + 0.0 (15131 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.08 x + 0.0 (15131 voxels, peak = 84), gca=83.9 gca peak = 0.12631 (89) mri peak = 0.12413 (93) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1917 voxels, overlap=0.389) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1917 voxels, peak = 96), gca=95.7 gca peak = 0.14500 (87) mri peak = 0.11172 (94) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2078 voxels, overlap=0.473) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2078 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.38462 (26) gca peak = 0.19357 (14) mri peak = 0.16996 (28) Fourth_Ventricle (15): linear fit = 1.68 x + 0.0 (218 voxels, overlap=0.177) Fourth_Ventricle (15): linear fit = 1.68 x + 0.0 (218 voxels, peak = 24), gca=23.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.32 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.46 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14686 (26) mri peak = 0.18979 (27) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1310 voxels, overlap=0.668) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1310 voxels, peak = 25), gca=24.6 gca peak = 0.13997 (19) mri peak = 0.16488 (30) Right_Lateral_Ventricle (43): linear fit = 1.38 x + 0.0 (1125 voxels, overlap=0.252) Right_Lateral_Ventricle (43): linear fit = 1.38 x + 0.0 (1125 voxels, peak = 26), gca=26.3 gca peak = 0.28167 (93) mri peak = 0.13060 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (803 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (803 voxels, peak = 93), gca=92.5 gca peak = 0.16597 (97) mri peak = 0.16726 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (696 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (696 voxels, peak = 97), gca=97.5 gca peak = 0.24040 (71) mri peak = 0.08333 (72) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (1173 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (1173 voxels, peak = 73), gca=73.5 gca peak = 0.27072 (73) mri peak = 0.09099 (77) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1128 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1128 voxels, peak = 72), gca=71.9 gca peak = 0.07767 (104) mri peak = 0.15523 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (51442 voxels, overlap=0.645) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (51442 voxels, peak = 104), gca=104.0 gca peak = 0.07908 (105) mri peak = 0.15966 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51860 voxels, overlap=0.533) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51860 voxels, peak = 105), gca=105.0 gca peak = 0.07293 (78) mri peak = 0.05527 (79) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (40973 voxels, overlap=0.911) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (40973 voxels, peak = 77), gca=76.8 gca peak = 0.08766 (78) mri peak = 0.05718 (80) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (39331 voxels, overlap=0.925) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (39331 voxels, peak = 78), gca=78.0 gca peak = 0.21552 (80) mri peak = 0.15706 (82) Right_Caudate (50): linear fit = 1.01 x + 0.0 (885 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (885 voxels, peak = 81), gca=81.2 gca peak = 0.12831 (75) mri peak = 0.17139 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (846 voxels, overlap=0.786) Left_Caudate (11): linear fit = 1.00 x + 0.0 (846 voxels, peak = 75), gca=75.0 gca peak = 0.10225 (78) mri peak = 0.06590 (79) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29863 voxels, overlap=0.929) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29863 voxels, peak = 78), gca=78.0 gca peak = 0.10829 (76) mri peak = 0.05989 (77) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31677 voxels, overlap=0.945) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31677 voxels, peak = 76), gca=75.6 gca peak = 0.15182 (92) mri peak = 0.13953 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7461 voxels, overlap=0.915) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7461 voxels, peak = 92), gca=91.5 gca peak = 0.15163 (90) mri peak = 0.09302 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6303 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6303 voxels, peak = 90), gca=89.6 gca peak = 0.28656 (76) mri peak = 0.10071 (74) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (568 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (568 voxels, peak = 76), gca=76.0 gca peak = 0.21987 (75) mri peak = 0.12414 (79) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (503 voxels, overlap=0.997) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (503 voxels, peak = 75), gca=75.0 gca peak = 0.11183 (94) mri peak = 0.09803 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5113 voxels, overlap=0.922) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5113 voxels, peak = 94), gca=93.5 gca peak = 0.10103 (89) mri peak = 0.10817 (92) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5156 voxels, overlap=0.832) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5156 voxels, peak = 88), gca=87.7 gca peak = 0.08274 (92) mri peak = 0.07780 (89) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2273 voxels, overlap=0.899) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2273 voxels, peak = 93), gca=93.4 gca peak = 0.08958 (85) mri peak = 0.08811 (88) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1952 voxels, overlap=0.946) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1952 voxels, peak = 85), gca=85.0 gca peak = 0.08870 (84) mri peak = 0.10941 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (15131 voxels, overlap=0.738) Brain_Stem (16): linear fit = 1.00 x + 0.0 (15131 voxels, peak = 84), gca=83.6 gca peak = 0.09705 (95) mri peak = 0.12413 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1917 voxels, overlap=0.788) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1917 voxels, peak = 95), gca=94.5 gca peak = 0.14342 (91) mri peak = 0.11172 (94) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (2078 voxels, overlap=0.866) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (2078 voxels, peak = 92), gca=92.4 gca peak = 0.12657 (37) mri peak = 0.38462 (26) gca peak = 0.14737 (22) mri peak = 0.16996 (28) Fourth_Ventricle (15): linear fit = 1.15 x + 0.0 (218 voxels, overlap=0.540) Fourth_Ventricle (15): linear fit = 1.15 x + 0.0 (218 voxels, peak = 25), gca=25.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.36646 (103) gca peak Third_Ventricle = 0.12657 (37) gca peak CSF = 0.16908 (53) gca peak Left_Accumbens_area = 0.45411 (68) gca peak Left_undetermined = 0.95280 (32) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12606 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.34643 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14506 (37) gca peak Fifth_Ventricle = 0.51669 (45) gca peak WM_hypointensities = 0.08020 (77) gca peak non_WM_hypointensities = 0.12165 (55) gca peak Optic_Chiasm = 0.68986 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.16 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 61208 voxels changed in iteration 0 of unlikely voxel relabeling 294 voxels changed in iteration 1 of unlikely voxel relabeling 24 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 69184 gm and wm labels changed (%34 to gray, %66 to white out of all changed labels) 506 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 69086 changed. image ll: -2.201, PF=0.500 pass 2: 18763 changed. image ll: -2.200, PF=0.500 pass 3: 5996 changed. pass 4: 2364 changed. 61311 voxels changed in iteration 0 of unlikely voxel relabeling 286 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7087 voxels changed in iteration 0 of unlikely voxel relabeling 104 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 4 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5126 voxels changed in iteration 0 of unlikely voxel relabeling 65 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4686 voxels changed in iteration 0 of unlikely voxel relabeling 27 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3644.903890 mri_ca_label stimesec 1.484774 mri_ca_label ru_maxrss 2098436 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 731313 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 480 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 777 mri_ca_label ru_nivcsw 5197 auto-labeling took 60 minutes and 2 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/transforms/cc_up.lta bert will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/norm.mgz 38784 voxels in left wm, 48124 in right wm, xrange [124, 133] searching rotation angles z=[-10 4], y=[-7 7] searching scale 1 Z rot -10.2 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 global minimum found at slice 128.4, rotations (0.46, -3.18) final transformation (x=128.4, yr=0.462, zr=-3.180): 0.99843 0.05547 0.00805 -6.61415; -0.05546 0.99846 -0.00045 36.32541; -0.00806 0.00000 0.99997 15.03905; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 99 114 eigenvectors: 0.00188 -0.01164 0.99993; -0.01228 -0.99986 -0.01162; 0.99992 -0.01226 -0.00203; writing aseg with callosum to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Wed Jan 18 21:43:09 EST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Jan 18 21:43:09 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE 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... 420 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 110 white matter peak found at 110 gm peak at 84 (84), valley at 46 (46) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 84 (84), valley at 21 (21) 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 2 minutes and 50 seconds. #-------------------------------------------- #@# Mask BFS Wed Jan 18 21:46:01 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1726388 voxels in mask (pct= 10.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jan 18 21:46:02 EST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.7 +- 5.9 [79.0 --> 125.0] GM (80.0) : 76.4 +- 13.4 [30.0 --> 95.0] setting bottom of white matter range to 89.8 setting top of gray matter range to 103.2 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... 6787 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4276 filled 9473 bright non-wm voxels segmented. 3047 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.41 minutes reading wm segmentation from wm.seg.mgz... 40 voxels added to wm to prevent paths from MTL structures to cortex 3685 additional wm voxels added 0 additional wm voxels added SEG EDIT: 45929 voxels turned on, 53893 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 17 found - 17 modified | TOTAL: 25 pass 2 (xy-): 0 found - 17 modified | TOTAL: 25 pass 1 (yz+): 24 found - 24 modified | TOTAL: 49 pass 2 (yz+): 0 found - 24 modified | TOTAL: 49 pass 1 (yz-): 21 found - 21 modified | TOTAL: 70 pass 2 (yz-): 0 found - 21 modified | TOTAL: 70 pass 1 (xz+): 14 found - 14 modified | TOTAL: 84 pass 2 (xz+): 0 found - 14 modified | TOTAL: 84 pass 1 (xz-): 14 found - 14 modified | TOTAL: 98 pass 2 (xz-): 0 found - 14 modified | TOTAL: 98 Iteration Number : 1 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 8 found - 8 modified | TOTAL: 18 pass 2 (+++): 0 found - 8 modified | TOTAL: 18 pass 1 (+++): 6 found - 6 modified | TOTAL: 24 pass 2 (+++): 0 found - 6 modified | TOTAL: 24 pass 1 (+++): 12 found - 12 modified | TOTAL: 36 pass 2 (+++): 0 found - 12 modified | TOTAL: 36 Iteration Number : 1 pass 1 (++): 51 found - 51 modified | TOTAL: 51 pass 2 (++): 0 found - 51 modified | TOTAL: 51 pass 1 (+-): 67 found - 67 modified | TOTAL: 118 pass 2 (+-): 0 found - 67 modified | TOTAL: 118 pass 1 (--): 68 found - 68 modified | TOTAL: 186 pass 2 (--): 0 found - 68 modified | TOTAL: 186 pass 1 (-+): 54 found - 54 modified | TOTAL: 240 pass 2 (-+): 0 found - 54 modified | TOTAL: 240 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 4 found - 4 modified | TOTAL: 10 pass 2 (yz-): 0 found - 4 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 2 found - 2 modified | TOTAL: 13 pass 2 (xz-): 0 found - 2 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 394 (out of 578214: 0.068141) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Jan 18 21:48:07 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.12555 0.03046 0.01970 -23.78674; -0.03666 1.02930 0.16892 -18.93918; -0.01848 -0.20713 0.86535 39.50741; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.12555 0.03046 0.01970 -23.78674; -0.03666 1.02930 0.16892 -18.93918; -0.01848 -0.20713 0.86535 39.50741; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 981 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 150), TAL = (2.0, 22.0, 8.0) talairach voxel to voxel transform 0.88726 -0.02917 -0.01450 21.12557; 0.02741 0.93392 -0.18292 25.56654; 0.02551 0.22292 1.11151 -39.08395; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 120, 150) --> (2.0, 22.0, 8.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, 22.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 22.00, 8.00) SRC: (111.27, 113.16, 157.15) search lh wm seed point around talairach space (-16.00, 22.00, 8.00), SRC: (143.22, 114.15, 158.07) 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 18 21:48:43 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 278476: 0.001436) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 523 vertices, 586 faces slice 40: 4597 vertices, 4790 faces slice 50: 11365 vertices, 11617 faces slice 60: 19470 vertices, 19787 faces slice 70: 29086 vertices, 29430 faces slice 80: 38909 vertices, 39228 faces slice 90: 48550 vertices, 48908 faces slice 100: 59385 vertices, 59763 faces slice 110: 69988 vertices, 70393 faces slice 120: 80356 vertices, 80761 faces slice 130: 90592 vertices, 90996 faces slice 140: 100215 vertices, 100584 faces slice 150: 107968 vertices, 108267 faces slice 160: 114185 vertices, 114498 faces slice 170: 120811 vertices, 121097 faces slice 180: 126770 vertices, 127017 faces slice 190: 131522 vertices, 131726 faces slice 200: 134752 vertices, 134865 faces slice 210: 134996 vertices, 135062 faces slice 220: 134996 vertices, 135062 faces slice 230: 134996 vertices, 135062 faces slice 240: 134996 vertices, 135062 faces slice 250: 134996 vertices, 135062 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; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 134996 voxel in cpt #1: X=-66 [v=134996,e=405186,f=270124] located at (-26.569817, -19.451679, 15.171679) For the whole surface: X=-66 [v=134996,e=405186,f=270124] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Jan 18 21:48:48 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2 (out of 278169: 0.000719) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 643 vertices, 726 faces slice 40: 4415 vertices, 4593 faces slice 50: 11332 vertices, 11586 faces slice 60: 19782 vertices, 20077 faces slice 70: 29827 vertices, 30194 faces slice 80: 39804 vertices, 40131 faces slice 90: 49854 vertices, 50233 faces slice 100: 61135 vertices, 61532 faces slice 110: 71307 vertices, 71713 faces slice 120: 81754 vertices, 82147 faces slice 130: 91228 vertices, 91601 faces slice 140: 99988 vertices, 100308 faces slice 150: 107133 vertices, 107414 faces slice 160: 113193 vertices, 113467 faces slice 170: 119759 vertices, 120033 faces slice 180: 125642 vertices, 125895 faces slice 190: 130515 vertices, 130728 faces slice 200: 133901 vertices, 134022 faces slice 210: 134322 vertices, 134380 faces slice 220: 134322 vertices, 134380 faces slice 230: 134322 vertices, 134380 faces slice 240: 134322 vertices, 134380 faces slice 250: 134322 vertices, 134380 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; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 134322 voxel in cpt #1: X=-58 [v=134322,e=403140,f=268760] located at (26.214954, -20.078960, 18.019379) For the whole surface: X=-58 [v=134322,e=403140,f=268760] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jan 18 21:48:53 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Wed Jan 18 21:48:53 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 4815 of (4815 4818) to complete... Waiting for PID 4818 of (4815 4818) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (4815 4818) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Wed Jan 18 21:48:58 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Wed Jan 18 21:48:58 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 4958 of (4958 4961) to complete... Waiting for PID 4961 of (4958 4961) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.8 mm, total surface area = 72423 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 53.643844 mris_inflate stimesec 0.413937 mris_inflate ru_maxrss 208616 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31424 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 576 mris_inflate ru_oublock 9512 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 71790 mris_inflate ru_nivcsw 275 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.9 mm, total surface area = 72591 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.149 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.034 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 53.500866 mris_inflate stimesec 0.428934 mris_inflate ru_maxrss 207720 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31202 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9464 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 71419 mris_inflate ru_nivcsw 294 PIDs (4958 4961) completed and logs appended. #-------------------------------------------- #@# QSphere lh Wed Jan 18 21:49:19 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Wed Jan 18 21:49:19 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 5099 of (5099 5102) to complete... Waiting for PID 5102 of (5099 5102) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.59 (0.00-->6.67) (max @ vno 51379 --> 51380) face area 0.02 +- 0.03 (-0.11-->0.56) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.816, avgs=0 005/300: dt: 0.9000, rms radial error=177.557, avgs=0 010/300: dt: 0.9000, rms radial error=177.000, avgs=0 015/300: dt: 0.9000, rms radial error=176.267, avgs=0 020/300: dt: 0.9000, rms radial error=175.432, avgs=0 025/300: dt: 0.9000, rms radial error=174.537, avgs=0 030/300: dt: 0.9000, rms radial error=173.609, avgs=0 035/300: dt: 0.9000, rms radial error=172.664, avgs=0 040/300: dt: 0.9000, rms radial error=171.711, avgs=0 045/300: dt: 0.9000, rms radial error=170.756, avgs=0 050/300: dt: 0.9000, rms radial error=169.802, avgs=0 055/300: dt: 0.9000, rms radial error=168.850, avgs=0 060/300: dt: 0.9000, rms radial error=167.902, avgs=0 065/300: dt: 0.9000, rms radial error=166.959, avgs=0 070/300: dt: 0.9000, rms radial error=166.020, avgs=0 075/300: dt: 0.9000, rms radial error=165.087, avgs=0 080/300: dt: 0.9000, rms radial error=164.158, avgs=0 085/300: dt: 0.9000, rms radial error=163.235, avgs=0 090/300: dt: 0.9000, rms radial error=162.316, avgs=0 095/300: dt: 0.9000, rms radial error=161.402, avgs=0 100/300: dt: 0.9000, rms radial error=160.493, avgs=0 105/300: dt: 0.9000, rms radial error=159.589, avgs=0 110/300: dt: 0.9000, rms radial error=158.690, avgs=0 115/300: dt: 0.9000, rms radial error=157.796, avgs=0 120/300: dt: 0.9000, rms radial error=156.907, avgs=0 125/300: dt: 0.9000, rms radial error=156.022, 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=153.406, avgs=0 145/300: dt: 0.9000, rms radial error=152.546, avgs=0 150/300: dt: 0.9000, rms radial error=151.691, avgs=0 155/300: dt: 0.9000, rms radial error=150.840, avgs=0 160/300: dt: 0.9000, rms radial error=149.994, avgs=0 165/300: dt: 0.9000, rms radial error=149.152, avgs=0 170/300: dt: 0.9000, rms radial error=148.315, avgs=0 175/300: dt: 0.9000, rms radial error=147.483, avgs=0 180/300: dt: 0.9000, rms radial error=146.655, avgs=0 185/300: dt: 0.9000, rms radial error=145.831, avgs=0 190/300: dt: 0.9000, rms radial error=145.012, avgs=0 195/300: dt: 0.9000, rms radial error=144.198, avgs=0 200/300: dt: 0.9000, rms radial error=143.388, avgs=0 205/300: dt: 0.9000, rms radial error=142.582, avgs=0 210/300: dt: 0.9000, rms radial error=141.781, avgs=0 215/300: dt: 0.9000, rms radial error=140.985, avgs=0 220/300: dt: 0.9000, rms radial error=140.192, avgs=0 225/300: dt: 0.9000, rms radial error=139.404, avgs=0 230/300: dt: 0.9000, rms radial error=138.621, avgs=0 235/300: dt: 0.9000, rms radial error=137.841, avgs=0 240/300: dt: 0.9000, rms radial error=137.066, avgs=0 245/300: dt: 0.9000, rms radial error=136.295, avgs=0 250/300: dt: 0.9000, rms radial error=135.529, avgs=0 255/300: dt: 0.9000, rms radial error=134.767, avgs=0 260/300: dt: 0.9000, rms radial error=134.009, avgs=0 265/300: dt: 0.9000, rms radial error=133.255, avgs=0 270/300: dt: 0.9000, rms radial error=132.505, avgs=0 275/300: dt: 0.9000, rms radial error=131.760, avgs=0 280/300: dt: 0.9000, rms radial error=131.019, avgs=0 285/300: dt: 0.9000, rms radial error=130.281, avgs=0 290/300: dt: 0.9000, rms radial error=129.548, avgs=0 295/300: dt: 0.9000, rms radial error=128.819, avgs=0 300/300: dt: 0.9000, rms radial error=128.094, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16081.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2803.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 3 (K=160.0), pass 1, starting sse = 317.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00748 epoch 4 (K=640.0), pass 1, starting sse = 21.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.28/24 = 0.01148 final distance error %28.28 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 342.242971 mris_sphere stimesec 0.507922 mris_sphere ru_maxrss 208824 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30976 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9544 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 74284 mris_sphere ru_nivcsw 873 FSRUNTIME@ mris_sphere 0.0407 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.60 (0.00-->7.78) (max @ vno 57353 --> 58594) face area 0.02 +- 0.03 (-0.21-->0.52) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.772, avgs=0 005/300: dt: 0.9000, rms radial error=177.511, avgs=0 010/300: dt: 0.9000, rms radial error=176.951, avgs=0 015/300: dt: 0.9000, rms radial error=176.215, avgs=0 020/300: dt: 0.9000, rms radial error=175.376, avgs=0 025/300: dt: 0.9000, rms radial error=174.480, avgs=0 030/300: dt: 0.9000, rms radial error=173.553, avgs=0 035/300: dt: 0.9000, rms radial error=172.609, avgs=0 040/300: dt: 0.9000, rms radial error=171.659, avgs=0 045/300: dt: 0.9000, rms radial error=170.705, avgs=0 050/300: dt: 0.9000, rms radial error=169.753, avgs=0 055/300: dt: 0.9000, rms radial error=168.804, avgs=0 060/300: dt: 0.9000, rms radial error=167.858, avgs=0 065/300: dt: 0.9000, rms radial error=166.917, avgs=0 070/300: dt: 0.9000, rms radial error=165.980, avgs=0 075/300: dt: 0.9000, rms radial error=165.048, avgs=0 080/300: dt: 0.9000, rms radial error=164.121, avgs=0 085/300: dt: 0.9000, rms radial error=163.200, avgs=0 090/300: dt: 0.9000, rms radial error=162.283, avgs=0 095/300: dt: 0.9000, rms radial error=161.371, avgs=0 100/300: dt: 0.9000, rms radial error=160.465, avgs=0 105/300: dt: 0.9000, rms radial error=159.563, avgs=0 110/300: dt: 0.9000, rms radial error=158.667, avgs=0 115/300: dt: 0.9000, rms radial error=157.775, avgs=0 120/300: dt: 0.9000, rms radial error=156.887, avgs=0 125/300: dt: 0.9000, rms radial error=156.005, avgs=0 130/300: dt: 0.9000, rms radial error=155.128, avgs=0 135/300: dt: 0.9000, rms radial error=154.255, avgs=0 140/300: dt: 0.9000, rms radial error=153.387, avgs=0 145/300: dt: 0.9000, rms radial error=152.525, avgs=0 150/300: dt: 0.9000, rms radial error=151.667, avgs=0 155/300: dt: 0.9000, rms radial error=150.814, avgs=0 160/300: dt: 0.9000, rms radial error=149.965, avgs=0 165/300: dt: 0.9000, rms radial error=149.122, avgs=0 170/300: dt: 0.9000, rms radial error=148.283, avgs=0 175/300: dt: 0.9000, rms radial error=147.448, avgs=0 180/300: dt: 0.9000, rms radial error=146.619, avgs=0 185/300: dt: 0.9000, rms radial error=145.794, avgs=0 190/300: dt: 0.9000, rms radial error=144.973, avgs=0 195/300: dt: 0.9000, rms radial error=144.157, avgs=0 200/300: dt: 0.9000, rms radial error=143.346, avgs=0 205/300: dt: 0.9000, rms radial error=142.539, avgs=0 210/300: dt: 0.9000, rms radial error=141.737, avgs=0 215/300: dt: 0.9000, rms radial error=140.939, avgs=0 220/300: dt: 0.9000, rms radial error=140.147, avgs=0 225/300: dt: 0.9000, rms radial error=139.360, avgs=0 230/300: dt: 0.9000, rms radial error=138.577, avgs=0 235/300: dt: 0.9000, rms radial error=137.799, avgs=0 240/300: dt: 0.9000, rms radial error=137.025, avgs=0 245/300: dt: 0.9000, rms radial error=136.255, avgs=0 250/300: dt: 0.9000, rms radial error=135.490, avgs=0 255/300: dt: 0.9000, rms radial error=134.729, avgs=0 260/300: dt: 0.9000, rms radial error=133.972, avgs=0 265/300: dt: 0.9000, rms radial error=133.219, avgs=0 270/300: dt: 0.9000, rms radial error=132.471, avgs=0 275/300: dt: 0.9000, rms radial error=131.726, avgs=0 280/300: dt: 0.9000, rms radial error=130.986, avgs=0 285/300: dt: 0.9000, rms radial error=130.250, avgs=0 290/300: dt: 0.9000, rms radial error=129.518, avgs=0 295/300: dt: 0.9000, rms radial error=128.790, avgs=0 300/300: dt: 0.9000, rms radial error=128.066, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16006.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2800.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 314.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00593 epoch 4 (K=640.0), pass 1, starting sse = 19.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/15 = 0.00994 final distance error %29.53 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 305.614539 mris_sphere stimesec 0.560914 mris_sphere ru_maxrss 207932 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 31253 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9496 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 73352 mris_sphere ru_nivcsw 856 FSRUNTIME@ mris_sphere 0.0365 hours 1 threads PIDs (5099 5102) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Wed Jan 18 21:51:45 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Wed Jan 18 21:51:45 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Jan 18 21:51:46 EST 2017 mris_fix_topology -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 bert lh #@# Fix Topology rh Wed Jan 18 21:51:46 EST 2017 mris_fix_topology -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 bert rh Waiting for PID 5835 of (5835 5838) to complete... Waiting for PID 5838 of (5835 5838) to complete... mris_fix_topology -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 bert lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-66 (nv=134996, nf=270124, ne=405186, 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 9 iterations marking ambiguous vertices... 3727 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 40 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6865 (-4.3433) -vertex loglikelihood: -5.5101 (-2.7550) -normal dot loglikelihood: -3.5738 (-3.5738) -quad curv loglikelihood: -6.4598 (-3.2299) Total Loglikelihood : -24.2302 CORRECTING DEFECT 0 (vertices=34, convex hull=79, v0=4462) After retessellation of defect 0 (v0=4462), euler #=-37 (132701,397085,264347) : difference with theory (-37) = 0 CORRECTING DEFECT 1 (vertices=28, convex hull=84, v0=7170) After retessellation of defect 1 (v0=7170), euler #=-36 (132710,397148,264402) : difference with theory (-36) = 0 CORRECTING DEFECT 2 (vertices=35, convex hull=69, v0=17767) After retessellation of defect 2 (v0=17767), euler #=-35 (132734,397246,264477) : difference with theory (-35) = 0 CORRECTING DEFECT 3 (vertices=59, convex hull=78, v0=19460) After retessellation of defect 3 (v0=19460), euler #=-34 (132767,397379,264578) : difference with theory (-34) = 0 CORRECTING DEFECT 4 (vertices=23, convex hull=36, v0=21076) After retessellation of defect 4 (v0=21076), euler #=-33 (132772,397404,264599) : difference with theory (-33) = 0 CORRECTING DEFECT 5 (vertices=17, convex hull=59, v0=25425) After retessellation of defect 5 (v0=25425), euler #=-32 (132781,397452,264639) : difference with theory (-32) = 0 CORRECTING DEFECT 6 (vertices=69, convex hull=106, v0=26960) After retessellation of defect 6 (v0=26960), euler #=-31 (132827,397635,264777) : difference with theory (-31) = 0 CORRECTING DEFECT 7 (vertices=25, convex hull=63, v0=38122) After retessellation of defect 7 (v0=38122), euler #=-30 (132839,397694,264825) : difference with theory (-30) = 0 CORRECTING DEFECT 8 (vertices=29, convex hull=29, v0=47939) After retessellation of defect 8 (v0=47939), euler #=-29 (132841,397711,264841) : difference with theory (-29) = 0 CORRECTING DEFECT 9 (vertices=5, convex hull=15, v0=48298) After retessellation of defect 9 (v0=48298), euler #=-28 (132842,397717,264847) : difference with theory (-28) = 0 CORRECTING DEFECT 10 (vertices=14, convex hull=33, v0=55772) After retessellation of defect 10 (v0=55772), euler #=-26 (132845,397737,264866) : difference with theory (-27) = -1 CORRECTING DEFECT 11 (vertices=5, convex hull=31, v0=57790) After retessellation of defect 11 (v0=57790), euler #=-25 (132847,397751,264879) : difference with theory (-26) = -1 CORRECTING DEFECT 12 (vertices=34, convex hull=63, v0=57995) After retessellation of defect 12 (v0=57995), euler #=-24 (132856,397801,264921) : difference with theory (-25) = -1 CORRECTING DEFECT 13 (vertices=9, convex hull=27, v0=62462) After retessellation of defect 13 (v0=62462), euler #=-23 (132857,397813,264933) : difference with theory (-24) = -1 CORRECTING DEFECT 14 (vertices=486, convex hull=167, v0=67344) After retessellation of defect 14 (v0=67344), euler #=-22 (132903,398034,265109) : difference with theory (-23) = -1 CORRECTING DEFECT 15 (vertices=34, convex hull=71, v0=71592) After retessellation of defect 15 (v0=71592), euler #=-21 (132922,398114,265171) : difference with theory (-22) = -1 CORRECTING DEFECT 16 (vertices=43, convex hull=79, v0=74391) After retessellation of defect 16 (v0=74391), euler #=-20 (132944,398211,265247) : difference with theory (-21) = -1 CORRECTING DEFECT 17 (vertices=6, convex hull=20, v0=79973) After retessellation of defect 17 (v0=79973), euler #=-19 (132945,398220,265256) : difference with theory (-20) = -1 CORRECTING DEFECT 18 (vertices=49, convex hull=85, v0=84011) After retessellation of defect 18 (v0=84011), euler #=-18 (132966,398317,265333) : difference with theory (-19) = -1 CORRECTING DEFECT 19 (vertices=44, convex hull=93, v0=86398) After retessellation of defect 19 (v0=86398), euler #=-17 (132999,398455,265439) : difference with theory (-18) = -1 CORRECTING DEFECT 20 (vertices=119, convex hull=50, v0=87225) After retessellation of defect 20 (v0=87225), euler #=-16 (133008,398505,265481) : difference with theory (-17) = -1 CORRECTING DEFECT 21 (vertices=37, convex hull=62, v0=87459) After retessellation of defect 21 (v0=87459), euler #=-15 (133024,398577,265538) : difference with theory (-16) = -1 CORRECTING DEFECT 22 (vertices=115, convex hull=139, v0=89099) After retessellation of defect 22 (v0=89099), euler #=-14 (133093,398845,265738) : difference with theory (-15) = -1 CORRECTING DEFECT 23 (vertices=8, convex hull=25, v0=89124) After retessellation of defect 23 (v0=89124), euler #=-13 (133096,398862,265753) : difference with theory (-14) = -1 CORRECTING DEFECT 24 (vertices=142, convex hull=101, v0=92193) After retessellation of defect 24 (v0=92193), euler #=-13 (133131,399022,265878) : difference with theory (-13) = 0 CORRECTING DEFECT 25 (vertices=60, convex hull=28, v0=94990) After retessellation of defect 25 (v0=94990), euler #=-12 (133139,399054,265903) : difference with theory (-12) = 0 CORRECTING DEFECT 26 (vertices=59, convex hull=59, v0=95080) After retessellation of defect 26 (v0=95080), euler #=-11 (133148,399104,265945) : difference with theory (-11) = 0 CORRECTING DEFECT 27 (vertices=58, convex hull=57, v0=97146) After retessellation of defect 27 (v0=97146), euler #=-10 (133157,399149,265982) : difference with theory (-10) = 0 CORRECTING DEFECT 28 (vertices=29, convex hull=38, v0=101701) After retessellation of defect 28 (v0=101701), euler #=-9 (133159,399170,266002) : difference with theory (-9) = 0 CORRECTING DEFECT 29 (vertices=41, convex hull=51, v0=103217) After retessellation of defect 29 (v0=103217), euler #=-8 (133183,399265,266074) : difference with theory (-8) = 0 CORRECTING DEFECT 30 (vertices=39, convex hull=74, v0=103296) After retessellation of defect 30 (v0=103296), euler #=-7 (133205,399365,266153) : difference with theory (-7) = 0 CORRECTING DEFECT 31 (vertices=65, convex hull=97, v0=107914) After retessellation of defect 31 (v0=107914), euler #=-6 (133236,399500,266258) : difference with theory (-6) = 0 CORRECTING DEFECT 32 (vertices=76, convex hull=73, v0=111517) After retessellation of defect 32 (v0=111517), euler #=-5 (133254,399582,266323) : difference with theory (-5) = 0 CORRECTING DEFECT 33 (vertices=81, convex hull=93, v0=112769) After retessellation of defect 33 (v0=112769), euler #=-4 (133291,399735,266440) : difference with theory (-4) = 0 CORRECTING DEFECT 34 (vertices=30, convex hull=74, v0=120061) After retessellation of defect 34 (v0=120061), euler #=-3 (133299,399790,266488) : difference with theory (-3) = 0 CORRECTING DEFECT 35 (vertices=41, convex hull=29, v0=123802) After retessellation of defect 35 (v0=123802), euler #=-2 (133304,399819,266513) : difference with theory (-2) = 0 CORRECTING DEFECT 36 (vertices=39, convex hull=78, v0=130125) After retessellation of defect 36 (v0=130125), euler #=-1 (133318,399892,266573) : difference with theory (-1) = 0 CORRECTING DEFECT 37 (vertices=128, convex hull=66, v0=130260) After retessellation of defect 37 (v0=130260), euler #=0 (133340,399989,266649) : difference with theory (0) = 0 CORRECTING DEFECT 38 (vertices=68, convex hull=45, v0=132252) After retessellation of defect 38 (v0=132252), euler #=1 (133345,400023,266679) : difference with theory (1) = 0 CORRECTING DEFECT 39 (vertices=29, convex hull=22, v0=134960) After retessellation of defect 39 (v0=134960), euler #=2 (133349,400041,266694) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.07-->7.40) (max @ vno 128626 --> 130432) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.07-->7.40) (max @ vno 128626 --> 130432) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 149 mutations (37.9%), 244 crossovers (62.1%), 157 vertices were eliminated building final representation... 1647 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133349, nf=266694, ne=400041, g=0) writing corrected surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.6 minutes 0 defective edges removing intersecting faces 000: 210 intersecting mris_fix_topology utimesec 1300.655270 mris_fix_topology stimesec 0.255961 mris_fix_topology ru_maxrss 430928 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 53373 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 624 mris_fix_topology ru_oublock 12744 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 3778 mris_fix_topology ru_nivcsw 3039 FSRUNTIME@ mris_fix_topology lh 0.3595 hours 1 threads mris_fix_topology -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 bert rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-58 (nv=134322, nf=268760, ne=403140, g=30) 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 12 iterations marking ambiguous vertices... 3070 ambiguous faces found in tessellation segmenting defects... 30 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 30 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7241 (-4.3621) -vertex loglikelihood: -5.4987 (-2.7493) -normal dot loglikelihood: -3.6276 (-3.6276) -quad curv loglikelihood: -6.3677 (-3.1838) Total Loglikelihood : -24.2180 CORRECTING DEFECT 0 (vertices=39, convex hull=87, v0=2588) After retessellation of defect 0 (v0=2588), euler #=-27 (132384,396141,263730) : difference with theory (-27) = 0 CORRECTING DEFECT 1 (vertices=30, convex hull=58, v0=12954) After retessellation of defect 1 (v0=12954), euler #=-26 (132394,396196,263776) : difference with theory (-26) = 0 CORRECTING DEFECT 2 (vertices=55, convex hull=97, v0=31931) After retessellation of defect 2 (v0=31931), euler #=-25 (132435,396359,263899) : difference with theory (-25) = 0 CORRECTING DEFECT 3 (vertices=59, convex hull=100, v0=32751) After retessellation of defect 3 (v0=32751), euler #=-24 (132475,396523,264024) : difference with theory (-24) = 0 CORRECTING DEFECT 4 (vertices=9, convex hull=23, v0=33505) After retessellation of defect 4 (v0=33505), euler #=-23 (132476,396535,264036) : difference with theory (-23) = 0 CORRECTING DEFECT 5 (vertices=54, convex hull=89, v0=39122) After retessellation of defect 5 (v0=39122), euler #=-22 (132501,396650,264127) : difference with theory (-22) = 0 CORRECTING DEFECT 6 (vertices=30, convex hull=77, v0=39275) After retessellation of defect 6 (v0=39275), euler #=-21 (132512,396716,264183) : difference with theory (-21) = 0 CORRECTING DEFECT 7 (vertices=60, convex hull=82, v0=40716) After retessellation of defect 7 (v0=40716), euler #=-20 (132543,396842,264279) : difference with theory (-20) = 0 CORRECTING DEFECT 8 (vertices=287, convex hull=229, v0=49549) After retessellation of defect 8 (v0=49549), euler #=-19 (132616,397178,264543) : difference with theory (-19) = 0 CORRECTING DEFECT 9 (vertices=55, convex hull=69, v0=53416) After retessellation of defect 9 (v0=53416), euler #=-18 (132624,397231,264589) : difference with theory (-18) = 0 CORRECTING DEFECT 10 (vertices=31, convex hull=28, v0=57084) After retessellation of defect 10 (v0=57084), euler #=-17 (132631,397261,264613) : difference with theory (-17) = 0 CORRECTING DEFECT 11 (vertices=33, convex hull=62, v0=63949) After retessellation of defect 11 (v0=63949), euler #=-16 (132640,397312,264656) : difference with theory (-16) = 0 CORRECTING DEFECT 12 (vertices=74, convex hull=121, v0=66772) After retessellation of defect 12 (v0=66772), euler #=-15 (132681,397492,264796) : difference with theory (-15) = 0 CORRECTING DEFECT 13 (vertices=238, convex hull=174, v0=68822) After retessellation of defect 13 (v0=68822), euler #=-14 (132753,397796,265029) : difference with theory (-14) = 0 CORRECTING DEFECT 14 (vertices=62, convex hull=87, v0=73909) After retessellation of defect 14 (v0=73909), euler #=-13 (132792,397950,265145) : difference with theory (-13) = 0 CORRECTING DEFECT 15 (vertices=127, convex hull=107, v0=85494) After retessellation of defect 15 (v0=85494), euler #=-12 (132813,398064,265239) : difference with theory (-12) = 0 CORRECTING DEFECT 16 (vertices=79, convex hull=36, v0=87265) After retessellation of defect 16 (v0=87265), euler #=-11 (132821,398102,265270) : difference with theory (-11) = 0 CORRECTING DEFECT 17 (vertices=17, convex hull=26, v0=94577) After retessellation of defect 17 (v0=94577), euler #=-10 (132825,398122,265287) : difference with theory (-10) = 0 CORRECTING DEFECT 18 (vertices=102, convex hull=99, v0=94653) After retessellation of defect 18 (v0=94653), euler #=-9 (132862,398276,265405) : difference with theory (-9) = 0 CORRECTING DEFECT 19 (vertices=16, convex hull=45, v0=100580) After retessellation of defect 19 (v0=100580), euler #=-8 (132864,398300,265428) : difference with theory (-8) = 0 CORRECTING DEFECT 20 (vertices=7, convex hull=25, v0=100599) After retessellation of defect 20 (v0=100599), euler #=-7 (132865,398309,265437) : difference with theory (-7) = 0 CORRECTING DEFECT 21 (vertices=36, convex hull=62, v0=101276) After retessellation of defect 21 (v0=101276), euler #=-6 (132883,398386,265497) : difference with theory (-6) = 0 CORRECTING DEFECT 22 (vertices=40, convex hull=84, v0=102155) After retessellation of defect 22 (v0=102155), euler #=-5 (132905,398486,265576) : difference with theory (-5) = 0 CORRECTING DEFECT 23 (vertices=61, convex hull=106, v0=105790) After retessellation of defect 23 (v0=105790), euler #=-4 (132936,398625,265685) : difference with theory (-4) = 0 CORRECTING DEFECT 24 (vertices=88, convex hull=93, v0=110282) After retessellation of defect 24 (v0=110282), euler #=-3 (132957,398729,265769) : difference with theory (-3) = 0 CORRECTING DEFECT 25 (vertices=6, convex hull=29, v0=117853) After retessellation of defect 25 (v0=117853), euler #=-2 (132957,398737,265778) : difference with theory (-2) = 0 CORRECTING DEFECT 26 (vertices=93, convex hull=64, v0=119730) After retessellation of defect 26 (v0=119730), euler #=-1 (132979,398829,265849) : difference with theory (-1) = 0 CORRECTING DEFECT 27 (vertices=22, convex hull=60, v0=121051) After retessellation of defect 27 (v0=121051), euler #=0 (132988,398879,265891) : difference with theory (0) = 0 CORRECTING DEFECT 28 (vertices=34, convex hull=65, v0=128258) After retessellation of defect 28 (v0=128258), euler #=1 (133000,398940,265941) : difference with theory (1) = 0 CORRECTING DEFECT 29 (vertices=113, convex hull=114, v0=129234) After retessellation of defect 29 (v0=129234), euler #=2 (133018,399048,266032) : 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-->11.97) (max @ vno 74254 --> 81332) 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-->11.97) (max @ vno 74254 --> 81332) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 95 mutations (34.7%), 179 crossovers (65.3%), 181 vertices were eliminated building final representation... 1304 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133018, nf=266032, ne=399048, g=0) writing corrected surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.3 minutes 0 defective edges removing intersecting faces 000: 206 intersecting 001: 5 intersecting mris_fix_topology utimesec 1044.125268 mris_fix_topology stimesec 0.191970 mris_fix_topology ru_maxrss 427276 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 54012 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 12680 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 2628 mris_fix_topology ru_nivcsw 2166 FSRUNTIME@ mris_fix_topology rh 0.2881 hours 1 threads PIDs (5835 5838) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 133349 - 400041 + 266694 = 2 --> 0 holes F =2V-4: 266694 = 266698-4 (0) 2E=3F: 800082 = 800082 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 133018 - 399048 + 266032 = 2 --> 0 holes F =2V-4: 266032 = 266036-4 (0) 2E=3F: 798096 = 798096 (0) total defect index = 0 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 35 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jan 18 22:13:28 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert lh #-------------------------------------------- #@# Make White Surf rh Wed Jan 18 22:13:28 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert rh Waiting for PID 11680 of (11680 11683) to complete... Waiting for PID 11683 of (11680 11683) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert lh using white.preaparc as white matter name... 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 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... 21017 bright wm thresholded. 10805 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.orig... computing class statistics... border white: 257825 voxels (1.54%) border gray 278292 voxels (1.66%) WM (103.0): 103.1 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.0 +- 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 +- 0.21 (0.05-->3.09) (max @ vno 79366 --> 132883) face area 0.28 +- 0.12 (0.00-->1.92) mean absolute distance = 0.90 +- 1.08 3680 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=82+-7.0 mean inside = 100.0, mean outside = 88.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=89.4, 61 (61) missing vertices, mean dist 0.5 [0.8 (%28.1)->1.0 (%71.9))] %59 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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 (0.07-->4.16) (max @ vno 82239 --> 132883) face area 0.28 +- 0.13 (0.00-->2.13) mean absolute distance = 0.46 +- 0.71 4426 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2126996.5, rms=7.889 001: dt: 0.5000, sse=1395750.6, rms=5.835 (26.035%) 002: dt: 0.5000, sse=1011256.9, rms=4.355 (25.359%) 003: dt: 0.5000, sse=803855.3, rms=3.288 (24.518%) 004: dt: 0.5000, sse=700339.6, rms=2.572 (21.768%) 005: dt: 0.5000, sse=650644.6, rms=2.141 (16.761%) 006: dt: 0.5000, sse=628609.4, rms=1.910 (10.787%) 007: dt: 0.5000, sse=618446.1, rms=1.792 (6.198%) rms = 1.74, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=615542.0, rms=1.743 (2.694%) 009: dt: 0.2500, sse=583519.6, rms=1.235 (29.181%) 010: dt: 0.2500, sse=580087.1, rms=1.170 (5.265%) rms = 1.15, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=579418.8, rms=1.153 (1.393%) rms = 1.14, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=578786.6, rms=1.144 (0.834%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.0, 42 (3) missing vertices, mean dist -0.3 [0.5 (%72.5)->0.3 (%27.5))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=terri, 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 (0.09-->4.35) (max @ vno 82239 --> 132883) face area 0.36 +- 0.16 (0.00-->3.20) mean absolute distance = 0.33 +- 0.45 4588 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1054347.4, rms=3.789 013: dt: 0.5000, sse=825667.1, rms=2.332 (38.451%) 014: dt: 0.5000, sse=759033.2, rms=1.730 (25.811%) 015: dt: 0.5000, sse=737507.2, rms=1.475 (14.720%) 016: dt: 0.5000, sse=729608.5, rms=1.393 (5.612%) rms = 1.40, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=719643.2, rms=1.184 (14.971%) 018: dt: 0.2500, sse=714570.4, rms=1.071 (9.550%) rms = 1.03, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=712515.0, rms=1.034 (3.477%) rms = 1.02, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=711552.9, rms=1.016 (1.748%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.0, 51 (2) missing vertices, mean dist -0.2 [0.4 (%72.9)->0.2 (%27.1))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=terri, 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 (0.05-->4.46) (max @ vno 82239 --> 132883) face area 0.34 +- 0.16 (0.00-->3.32) mean absolute distance = 0.25 +- 0.34 3876 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=859839.9, rms=2.847 021: dt: 0.5000, sse=715101.1, rms=1.528 (46.352%) 022: dt: 0.5000, sse=691610.5, rms=1.208 (20.907%) 023: dt: 0.5000, sse=687986.9, rms=1.149 (4.923%) rms = 1.18, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=680015.6, rms=0.977 (14.988%) 025: dt: 0.2500, sse=677207.2, rms=0.907 (7.093%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=676510.2, rms=0.904 (0.370%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.6, 59 (1) 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=terri, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=684635.1, rms=1.314 027: dt: 0.5000, sse=658456.6, rms=0.829 (36.892%) rms = 1.00, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=654720.6, rms=0.743 (10.363%) rms = 0.73, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=654483.1, rms=0.733 (1.451%) rms = 0.73, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=653638.7, rms=0.728 (0.603%) positioning took 0.4 minutes generating cortex label... 5 non-cortical segments detected only using segment with 8353 vertices erasing segment 1 (vno[0] = 94669) erasing segment 2 (vno[0] = 97383) erasing segment 3 (vno[0] = 101538) erasing segment 4 (vno[0] = 133140) writing cortex label to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label... writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.area vertex spacing 0.89 +- 0.25 (0.05-->4.51) (max @ vno 82239 --> 132883) face area 0.34 +- 0.15 (0.00-->3.38) refinement took 4.2 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert rh using white.preaparc as white matter name... 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 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... 21017 bright wm thresholded. 10805 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.orig... computing class statistics... border white: 257825 voxels (1.54%) border gray 278292 voxels (1.66%) WM (103.0): 103.1 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.0 +- 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 (0.04-->3.90) (max @ vno 127406 --> 133012) face area 0.28 +- 0.12 (0.00-->2.95) mean absolute distance = 0.90 +- 1.06 3954 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 = 100.2, mean outside = 88.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=89.8, 11 (11) missing vertices, mean dist 0.5 [0.8 (%27.4)->0.9 (%72.6))] %57 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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 (0.11-->6.88) (max @ vno 132724 --> 74265) face area 0.28 +- 0.13 (0.00-->3.53) mean absolute distance = 0.46 +- 0.70 3981 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2087938.1, rms=7.788 001: dt: 0.5000, sse=1371920.0, rms=5.739 (26.305%) 002: dt: 0.5000, sse=993973.0, rms=4.259 (25.787%) 003: dt: 0.5000, sse=791705.3, rms=3.190 (25.101%) 004: dt: 0.5000, sse=690761.5, rms=2.465 (22.722%) 005: dt: 0.5000, sse=641241.2, rms=2.032 (17.576%) 006: dt: 0.5000, sse=620865.3, rms=1.806 (11.105%) 007: dt: 0.5000, sse=612426.4, rms=1.694 (6.202%) rms = 1.65, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=609209.2, rms=1.649 (2.694%) 009: dt: 0.2500, sse=583486.0, rms=1.183 (28.237%) 010: dt: 0.2500, sse=580519.4, rms=1.128 (4.655%) rms = 1.11, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=580099.1, rms=1.114 (1.236%) rms = 1.10, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=579590.2, rms=1.105 (0.855%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.3, 27 (1) missing vertices, mean dist -0.3 [0.5 (%72.6)->0.3 (%27.4))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=terri, 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 (0.14-->7.76) (max @ vno 132724 --> 74265) face area 0.36 +- 0.16 (0.00-->5.52) mean absolute distance = 0.33 +- 0.44 4500 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1048438.4, rms=3.759 013: dt: 0.5000, sse=820168.1, rms=2.298 (38.847%) 014: dt: 0.5000, sse=757661.2, rms=1.710 (25.598%) 015: dt: 0.5000, sse=736598.9, rms=1.454 (14.990%) 016: dt: 0.5000, sse=727019.3, rms=1.354 (6.895%) rms = 1.36, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=717784.8, rms=1.161 (14.223%) 018: dt: 0.2500, sse=713222.0, rms=1.056 (9.076%) rms = 1.02, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=711593.6, rms=1.022 (3.140%) rms = 1.01, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=711527.2, rms=1.007 (1.488%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=94.3, 36 (1) missing vertices, mean dist -0.2 [0.4 (%73.3)->0.2 (%26.7))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=terri, 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 (0.11-->7.88) (max @ vno 132724 --> 74265) face area 0.34 +- 0.16 (0.00-->5.42) mean absolute distance = 0.24 +- 0.34 3906 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=854522.4, rms=2.801 021: dt: 0.5000, sse=713132.4, rms=1.490 (46.806%) 022: dt: 0.5000, sse=690124.0, rms=1.176 (21.079%) 023: dt: 0.5000, sse=686404.3, rms=1.118 (4.928%) rms = 1.14, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=679339.6, rms=0.961 (13.994%) 025: dt: 0.2500, sse=677268.8, rms=0.902 (6.174%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=676587.5, rms=0.899 (0.356%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.9, 39 (1) missing vertices, mean dist -0.1 [0.3 (%57.5)->0.2 (%42.5))] %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=terri, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=681501.4, rms=1.256 027: dt: 0.5000, sse=659902.0, rms=0.797 (36.553%) rms = 0.97, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=654952.6, rms=0.726 (8.895%) rms = 0.73, time step reduction 2 of 3 to 0.125... rms = 0.72, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=654402.8, rms=0.721 (0.665%) positioning took 0.4 minutes generating cortex label... 6 non-cortical segments detected only using segment with 8167 vertices erasing segment 1 (vno[0] = 83698) erasing segment 2 (vno[0] = 90645) erasing segment 3 (vno[0] = 94129) erasing segment 4 (vno[0] = 97576) erasing segment 5 (vno[0] = 104770) writing cortex label to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label... writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.area vertex spacing 0.90 +- 0.25 (0.04-->7.95) (max @ vno 74265 --> 132724) face area 0.34 +- 0.16 (0.00-->5.35) refinement took 4.2 minutes PIDs (11680 11683) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Wed Jan 18 22:17:39 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Wed Jan 18 22:17:39 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 12831 of (12831 12834) to complete... Waiting for PID 12834 of (12831 12834) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm 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... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm 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... PIDs (12831 12834) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Wed Jan 18 22:17:43 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_inflate -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Wed Jan 18 22:17:43 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_inflate -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 12908 of (12908 12911) to complete... Waiting for PID 12911 of (12908 12911) to complete... mris_inflate -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.9 mm, total surface area = 81747 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.170 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 53.433876 mris_inflate stimesec 0.450931 mris_inflate ru_maxrss 206180 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30826 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10440 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 65440 mris_inflate ru_nivcsw 332 mris_inflate -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.1 mm, total surface area = 81956 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=0.069 (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=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 54.061781 mris_inflate stimesec 0.456930 mris_inflate ru_maxrss 205800 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30731 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10408 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 63357 mris_inflate ru_nivcsw 287 PIDs (12908 12911) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Wed Jan 18 22:18:04 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Wed Jan 18 22:18:04 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf mris_curvature -w rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf reconbatchjobs /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 13076 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13079 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13082 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13085 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13088 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13091 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13094 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13097 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13100 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13103 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13106 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... Waiting for PID 13109 of (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 2.575*4pi (32.354) --> -2 handles ICI = 139.0, FI = 1477.4, variation=23175.957 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 160 vertices thresholded to be in k1 ~ [-1.08 0.48], k2 ~ [-0.18 0.25] total integrated curvature = 0.555*4pi (6.975) --> 0 handles ICI = 1.5, FI = 8.7, variation=154.311 127 vertices thresholded to be in [-0.09 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 97 vertices thresholded to be in [-0.20 0.24] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = 4.307*4pi (54.128) --> -3 handles ICI = 138.7, FI = 1440.4, variation=22684.386 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 138 vertices thresholded to be in k1 ~ [-0.51 0.31], k2 ~ [-0.24 0.10] total integrated curvature = 0.471*4pi (5.918) --> 1 handles ICI = 1.4, FI = 8.5, variation=149.793 135 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 102 vertices thresholded to be in [-0.16 0.13] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.021 done. PIDs (13076 13079 13082 13085 13088 13091 13094 13097 13100 13103 13106 13109) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Wed Jan 18 22:19:12 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm bert lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/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 [ 232 ] Gb_filter = 0 WARN: S lookup min: -0.324806 WARN: S explicit min: 0.000000 vertex = 1 #----------------------------------------- #@# Curvature Stats rh Wed Jan 18 22:19:15 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm bert rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/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 [ 264 ] Gb_filter = 0 WARN: S lookup min: -0.300273 WARN: S explicit min: 0.000000 vertex = 108 #-------------------------------------------- #@# Sphere lh Wed Jan 18 22:19:19 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_sphere -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Wed Jan 18 22:19:19 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_sphere -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 13561 of (13561 13564) to complete... Waiting for PID 13564 of (13561 13564) to complete... mris_sphere -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.275... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=terri, 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 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.40 pass 1: epoch 2 of 3 starting distance error %20.35 unfolding complete - removing small folds... starting distance error %20.28 removing remaining folds... final distance error %20.29 MRISunfold() return, current seed 1234 -01: dt=0.0000, 124 negative triangles 185: dt=0.9900, 124 negative triangles 186: dt=0.9900, 77 negative triangles 187: dt=0.9900, 64 negative triangles 188: dt=0.9900, 59 negative triangles 189: dt=0.9900, 49 negative triangles 190: dt=0.9900, 44 negative triangles 191: dt=0.9900, 43 negative triangles 192: dt=0.9900, 48 negative triangles 193: dt=0.9900, 43 negative triangles 194: dt=0.9900, 40 negative triangles 195: dt=0.9900, 39 negative triangles 196: dt=0.9900, 38 negative triangles 197: dt=0.9900, 39 negative triangles 198: dt=0.9900, 33 negative triangles 199: dt=0.9900, 31 negative triangles 200: dt=0.9900, 28 negative triangles 201: dt=0.9900, 27 negative triangles 202: dt=0.9900, 27 negative triangles 203: dt=0.9900, 29 negative triangles 204: dt=0.9900, 29 negative triangles 205: dt=0.9900, 24 negative triangles 206: dt=0.9900, 27 negative triangles 207: dt=0.9900, 22 negative triangles 208: dt=0.9900, 24 negative triangles 209: dt=0.9900, 24 negative triangles 210: dt=0.9900, 27 negative triangles 211: dt=0.9900, 23 negative triangles 212: dt=0.9900, 27 negative triangles 213: dt=0.9900, 21 negative triangles 214: dt=0.9900, 18 negative triangles 215: dt=0.9900, 19 negative triangles 216: dt=0.9900, 22 negative triangles 217: dt=0.9900, 22 negative triangles 218: dt=0.9900, 19 negative triangles 219: dt=0.9900, 17 negative triangles 220: dt=0.9900, 20 negative triangles 221: dt=0.9900, 20 negative triangles 222: dt=0.9900, 23 negative triangles 223: dt=0.9900, 22 negative triangles 224: dt=0.9900, 21 negative triangles 225: dt=0.9900, 15 negative triangles 226: dt=0.9900, 23 negative triangles 227: dt=0.9900, 19 negative triangles 228: dt=0.9900, 21 negative triangles 229: dt=0.9900, 19 negative triangles 230: dt=0.9900, 20 negative triangles 231: dt=0.9900, 21 negative triangles 232: dt=0.9900, 17 negative triangles 233: dt=0.9900, 19 negative triangles 234: dt=0.9900, 19 negative triangles 235: dt=0.9405, 23 negative triangles 236: dt=0.9405, 19 negative triangles 237: dt=0.9405, 20 negative triangles 238: dt=0.9405, 19 negative triangles 239: dt=0.9405, 17 negative triangles 240: dt=0.9405, 20 negative triangles 241: dt=0.9405, 22 negative triangles 242: dt=0.9405, 24 negative triangles 243: dt=0.9405, 19 negative triangles 244: dt=0.9405, 16 negative triangles 245: dt=0.8935, 19 negative triangles 246: dt=0.8935, 16 negative triangles 247: dt=0.8935, 20 negative triangles 248: dt=0.8935, 22 negative triangles 249: dt=0.8935, 21 negative triangles 250: dt=0.8935, 21 negative triangles 251: dt=0.8935, 18 negative triangles 252: dt=0.8935, 19 negative triangles 253: dt=0.8935, 18 negative triangles 254: dt=0.8935, 20 negative triangles 255: dt=0.8488, 18 negative triangles 256: dt=0.8488, 20 negative triangles 257: dt=0.8488, 19 negative triangles 258: dt=0.8488, 19 negative triangles 259: dt=0.8488, 21 negative triangles 260: dt=0.8488, 17 negative triangles 261: dt=0.8488, 19 negative triangles 262: dt=0.8488, 18 negative triangles 263: dt=0.8488, 20 negative triangles 264: dt=0.8488, 20 negative triangles 265: dt=0.8064, 19 negative triangles 266: dt=0.8064, 18 negative triangles 267: dt=0.8064, 12 negative triangles 268: dt=0.8064, 16 negative triangles 269: dt=0.8064, 15 negative triangles 270: dt=0.8064, 18 negative triangles 271: dt=0.8064, 18 negative triangles 272: dt=0.8064, 17 negative triangles 273: dt=0.8064, 19 negative triangles 274: dt=0.8064, 15 negative triangles 275: dt=0.8064, 17 negative triangles 276: dt=0.8064, 17 negative triangles 277: dt=0.7660, 15 negative triangles 278: dt=0.7660, 13 negative triangles 279: dt=0.7660, 13 negative triangles 280: dt=0.7660, 15 negative triangles 281: dt=0.7660, 14 negative triangles 282: dt=0.7660, 9 negative triangles 283: dt=0.7660, 12 negative triangles 284: dt=0.7660, 12 negative triangles 285: dt=0.7660, 15 negative triangles 286: dt=0.7660, 17 negative triangles 287: dt=0.7660, 17 negative triangles 288: dt=0.7660, 14 negative triangles 289: dt=0.7660, 15 negative triangles 290: dt=0.7660, 12 negative triangles 291: dt=0.7660, 15 negative triangles 292: dt=0.7277, 10 negative triangles 293: dt=0.7277, 14 negative triangles 294: dt=0.7277, 12 negative triangles 295: dt=0.7277, 11 negative triangles 296: dt=0.7277, 10 negative triangles 297: dt=0.7277, 9 negative triangles 298: dt=0.7277, 10 negative triangles 299: dt=0.7277, 10 negative triangles 300: dt=0.7277, 9 negative triangles 301: dt=0.7277, 7 negative triangles 302: dt=0.7277, 10 negative triangles 303: dt=0.7277, 8 negative triangles 304: dt=0.7277, 12 negative triangles 305: dt=0.7277, 8 negative triangles 306: dt=0.7277, 11 negative triangles 307: dt=0.7277, 6 negative triangles 308: dt=0.7277, 8 negative triangles 309: dt=0.7277, 7 negative triangles 310: dt=0.7277, 3 negative triangles 311: dt=0.7277, 4 negative triangles 312: dt=0.7277, 5 negative triangles 313: dt=0.7277, 2 negative triangles 314: dt=0.7277, 2 negative triangles 315: dt=0.7277, 2 negative triangles 316: dt=0.7277, 5 negative triangles 317: dt=0.7277, 2 negative triangles 318: dt=0.7277, 1 negative triangles 319: dt=0.7277, 4 negative triangles 320: dt=0.7277, 3 negative triangles 321: dt=0.7277, 1 negative triangles 322: dt=0.7277, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.33 hours mris_sphere utimesec 4146.710604 mris_sphere stimesec 1.263807 mris_sphere ru_maxrss 288076 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 51899 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9440 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 119455 mris_sphere ru_nivcsw 7813 FSRUNTIME@ mris_sphere 0.3280 hours 1 threads mris_sphere -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.272... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=terri, 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 %20.20 pass 1: epoch 2 of 3 starting distance error %20.10 unfolding complete - removing small folds... starting distance error %20.06 removing remaining folds... final distance error %20.08 MRISunfold() return, current seed 1234 -01: dt=0.0000, 114 negative triangles 172: dt=0.9900, 114 negative triangles 173: dt=0.9900, 77 negative triangles 174: dt=0.9900, 65 negative triangles 175: dt=0.9900, 50 negative triangles 176: dt=0.9900, 43 negative triangles 177: dt=0.9900, 39 negative triangles 178: dt=0.9900, 40 negative triangles 179: dt=0.9900, 33 negative triangles 180: dt=0.9900, 38 negative triangles 181: dt=0.9900, 28 negative triangles 182: dt=0.9900, 35 negative triangles 183: dt=0.9900, 27 negative triangles 184: dt=0.9900, 29 negative triangles 185: dt=0.9900, 28 negative triangles 186: dt=0.9900, 24 negative triangles 187: dt=0.9900, 16 negative triangles 188: dt=0.9900, 17 negative triangles 189: dt=0.9900, 12 negative triangles 190: dt=0.9900, 11 negative triangles 191: dt=0.9900, 5 negative triangles 192: dt=0.9900, 13 negative triangles 193: dt=0.9900, 9 negative triangles 194: dt=0.9900, 7 negative triangles 195: dt=0.9900, 3 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 1 negative triangles 198: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.29 hours mris_sphere utimesec 3712.058681 mris_sphere stimesec 1.193818 mris_sphere ru_maxrss 287768 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 51823 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9384 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 119547 mris_sphere ru_nivcsw 7283 FSRUNTIME@ mris_sphere 0.2940 hours 1 threads PIDs (13561 13564) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Wed Jan 18 22:39:00 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_register -curv -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Wed Jan 18 22:39:00 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_register -curv -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 18744 of (18744 18747) to complete... Waiting for PID 18747 of (18744 18747) to complete... mris_register -curv -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts cmdline mris_register -curv -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=terri, 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=terri, 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 = 5.381 curvature mean = 0.018, std = 0.818 curvature mean = 0.015, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 289581.1, tmin=0.9440 d=32.00 min @ (0.00, 8.00, 0.00) sse = 270770.7, tmin=1.9120 d=16.00 min @ (4.00, -4.00, 4.00) sse = 226631.8, tmin=2.8802 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 226055.4, tmin=3.8961 d=4.00 min @ (1.00, 1.00, -1.00) sse = 224526.3, tmin=4.9312 d=2.00 min @ (0.00, -0.50, 0.50) sse = 224140.9, tmin=5.9756 d=0.50 min @ (0.00, -0.12, 0.00) sse = 224130.3, tmin=8.0061 tol=1.0e+00, sigma=0.5, host=terri, 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 8.01 min curvature mean = 0.003, std = 0.842 curvature mean = 0.006, std = 0.948 curvature mean = 0.002, std = 0.854 curvature mean = 0.002, std = 0.979 curvature mean = 0.002, std = 0.857 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.024, std = 0.273 curvature mean = 0.041, std = 0.248 curvature mean = 0.053, std = 0.373 curvature mean = 0.039, std = 0.307 curvature mean = 0.027, std = 0.570 curvature mean = 0.038, std = 0.335 curvature mean = 0.014, std = 0.707 curvature mean = 0.037, std = 0.347 curvature mean = 0.004, std = 0.808 MRISregister() return, current seed 0 -01: dt=0.0000, 81 negative triangles 109: dt=0.9900, 81 negative triangles 110: dt=0.9405, 85 negative triangles expanding nbhd size to 1 111: dt=0.9900, 85 negative triangles 112: dt=0.9900, 73 negative triangles 113: dt=0.9900, 65 negative triangles 114: dt=0.9900, 58 negative triangles 115: dt=0.9900, 53 negative triangles 116: dt=0.9900, 57 negative triangles 117: dt=0.9900, 59 negative triangles 118: dt=0.9900, 56 negative triangles 119: dt=0.9900, 54 negative triangles 120: dt=0.9900, 50 negative triangles 121: dt=0.9900, 55 negative triangles 122: dt=0.9900, 49 negative triangles 123: dt=0.9900, 46 negative triangles 124: dt=0.9900, 41 negative triangles 125: dt=0.9900, 44 negative triangles 126: dt=0.9900, 40 negative triangles 127: dt=0.9900, 43 negative triangles 128: dt=0.9900, 40 negative triangles 129: dt=0.9900, 39 negative triangles 130: dt=0.9900, 41 negative triangles 131: dt=0.9900, 39 negative triangles 132: dt=0.9900, 32 negative triangles 133: dt=0.9900, 30 negative triangles 134: dt=0.9900, 28 negative triangles 135: dt=0.9900, 25 negative triangles 136: dt=0.9900, 25 negative triangles 137: dt=0.9900, 23 negative triangles 138: dt=0.9900, 22 negative triangles 139: dt=0.9900, 24 negative triangles 140: dt=0.9900, 26 negative triangles 141: dt=0.9900, 26 negative triangles 142: dt=0.9900, 26 negative triangles 143: dt=0.9900, 24 negative triangles 144: dt=0.9900, 20 negative triangles 145: dt=0.9900, 20 negative triangles 146: dt=0.9900, 18 negative triangles 147: dt=0.9900, 16 negative triangles 148: dt=0.9900, 15 negative triangles 149: dt=0.9900, 16 negative triangles 150: dt=0.9900, 17 negative triangles 151: dt=0.9900, 13 negative triangles 152: dt=0.9900, 12 negative triangles 153: dt=0.9900, 12 negative triangles 154: dt=0.9900, 13 negative triangles 155: dt=0.9900, 13 negative triangles 156: dt=0.9900, 9 negative triangles 157: dt=0.9900, 6 negative triangles 158: dt=0.9900, 6 negative triangles 159: dt=0.9900, 3 negative triangles 160: dt=0.9900, 2 negative triangles 161: dt=0.9900, 3 negative triangles 162: dt=0.9900, 2 negative triangles 163: dt=0.9900, 1 negative triangles 164: dt=0.9900, 1 negative triangles 165: dt=0.9900, 2 negative triangles 166: dt=0.9900, 1 negative triangles 167: dt=0.9900, 1 negative triangles 168: dt=0.9900, 1 negative triangles 169: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.56 hours mris_register utimesec 5487.352795 mris_register stimesec 1.781729 mris_register ru_maxrss 261824 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 37820 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5584 mris_register ru_oublock 9472 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 138871 mris_register ru_nivcsw 11331 FSRUNTIME@ mris_register 0.5554 hours 1 threads mris_register -curv -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts cmdline mris_register -curv -rusage /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=terri, 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=terri, 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 = 5.468 curvature mean = 0.032, std = 0.817 curvature mean = 0.017, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 318030.2, tmin=0.9646 d=32.00 min @ (8.00, 0.00, 8.00) sse = 269173.2, tmin=1.9400 d=16.00 min @ (0.00, 4.00, -4.00) sse = 251491.6, tmin=2.9368 d=8.00 min @ (-2.00, -2.00, 2.00) sse = 242277.9, tmin=3.9565 d=4.00 min @ (0.00, 0.00, -1.00) sse = 241024.0, tmin=4.9619 d=2.00 min @ (0.50, 0.00, 0.00) sse = 240879.6, tmin=5.9616 d=1.00 min @ (-0.25, 0.25, 0.25) sse = 240804.6, tmin=6.9668 d=0.50 min @ (0.12, 0.00, 0.00) sse = 240781.5, tmin=7.9808 tol=1.0e+00, sigma=0.5, host=terri, 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 7.98 min curvature mean = 0.004, std = 0.831 curvature mean = 0.007, std = 0.949 curvature mean = 0.001, std = 0.839 curvature mean = 0.003, std = 0.980 curvature mean = 0.000, std = 0.840 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.025, std = 0.255 curvature mean = 0.037, std = 0.242 curvature mean = 0.060, std = 0.394 curvature mean = 0.033, std = 0.300 curvature mean = 0.029, std = 0.602 curvature mean = 0.033, std = 0.327 curvature mean = 0.014, std = 0.746 curvature mean = 0.033, std = 0.338 curvature mean = 0.004, std = 0.848 MRISregister() return, current seed 0 -01: dt=0.0000, 123 negative triangles 117: dt=0.9900, 123 negative triangles expanding nbhd size to 1 118: dt=0.9900, 130 negative triangles 119: dt=0.9900, 123 negative triangles 120: dt=0.9405, 123 negative triangles 121: dt=0.9405, 116 negative triangles 122: dt=0.9405, 116 negative triangles 123: dt=0.9405, 114 negative triangles 124: dt=0.9405, 111 negative triangles 125: dt=0.9405, 109 negative triangles 126: dt=0.9405, 111 negative triangles 127: dt=0.9405, 109 negative triangles 128: dt=0.9405, 108 negative triangles 129: dt=0.9405, 110 negative triangles 130: dt=0.9405, 107 negative triangles 131: dt=0.9405, 104 negative triangles 132: dt=0.9405, 104 negative triangles 133: dt=0.9405, 102 negative triangles 134: dt=0.9405, 104 negative triangles 135: dt=0.9405, 100 negative triangles 136: dt=0.9405, 100 negative triangles 137: dt=0.9405, 99 negative triangles 138: dt=0.9405, 98 negative triangles 139: dt=0.9405, 96 negative triangles 140: dt=0.9405, 94 negative triangles 141: dt=0.9405, 92 negative triangles 142: dt=0.9405, 90 negative triangles 143: dt=0.9405, 92 negative triangles 144: dt=0.9405, 89 negative triangles 145: dt=0.9405, 91 negative triangles 146: dt=0.9405, 88 negative triangles 147: dt=0.9405, 89 negative triangles 148: dt=0.9405, 95 negative triangles 149: dt=0.9405, 89 negative triangles 150: dt=0.9405, 88 negative triangles 151: dt=0.9405, 87 negative triangles 152: dt=0.9405, 91 negative triangles 153: dt=0.9405, 83 negative triangles 154: dt=0.9405, 84 negative triangles 155: dt=0.9405, 83 negative triangles 156: dt=0.9405, 85 negative triangles 157: dt=0.9405, 81 negative triangles 158: dt=0.9405, 81 negative triangles 159: dt=0.9405, 82 negative triangles 160: dt=0.9405, 80 negative triangles 161: dt=0.9405, 81 negative triangles 162: dt=0.9405, 80 negative triangles 163: dt=0.9405, 79 negative triangles 164: dt=0.9405, 80 negative triangles 165: dt=0.9405, 81 negative triangles 166: dt=0.9405, 81 negative triangles 167: dt=0.9405, 81 negative triangles 168: dt=0.9405, 78 negative triangles 169: dt=0.9405, 79 negative triangles 170: dt=0.9405, 79 negative triangles 171: dt=0.9405, 80 negative triangles 172: dt=0.9405, 77 negative triangles 173: dt=0.9405, 77 negative triangles 174: dt=0.9405, 79 negative triangles 175: dt=0.9405, 80 negative triangles 176: dt=0.9405, 80 negative triangles 177: dt=0.9405, 80 negative triangles 178: dt=0.9405, 82 negative triangles 179: dt=0.9405, 83 negative triangles 180: dt=0.9405, 83 negative triangles 181: dt=0.9405, 83 negative triangles 182: dt=0.8935, 81 negative triangles 183: dt=0.8935, 82 negative triangles 184: dt=0.8935, 81 negative triangles 185: dt=0.8935, 81 negative triangles 186: dt=0.8935, 83 negative triangles 187: dt=0.8935, 84 negative triangles 188: dt=0.8935, 83 negative triangles 189: dt=0.8935, 86 negative triangles 190: dt=0.8935, 85 negative triangles 191: dt=0.8935, 85 negative triangles 192: dt=0.8488, 81 negative triangles 193: dt=0.8488, 82 negative triangles 194: dt=0.8488, 78 negative triangles 195: dt=0.8488, 81 negative triangles 196: dt=0.8488, 81 negative triangles 197: dt=0.8488, 78 negative triangles 198: dt=0.8488, 79 negative triangles 199: dt=0.8488, 80 negative triangles 200: dt=0.8488, 80 negative triangles 201: dt=0.8488, 78 negative triangles 202: dt=0.8064, 79 negative triangles 203: dt=0.8064, 79 negative triangles 204: dt=0.8064, 79 negative triangles 205: dt=0.8064, 79 negative triangles 206: dt=0.8064, 78 negative triangles 207: dt=0.8064, 79 negative triangles 208: dt=0.8064, 78 negative triangles 209: dt=0.8064, 79 negative triangles 210: dt=0.8064, 84 negative triangles 211: dt=0.8064, 83 negative triangles 212: dt=0.7660, 81 negative triangles 213: dt=0.7660, 78 negative triangles 214: dt=0.7660, 78 negative triangles 215: dt=0.7660, 79 negative triangles 216: dt=0.7660, 80 negative triangles 217: dt=0.7660, 80 negative triangles 218: dt=0.7660, 79 negative triangles 219: dt=0.7660, 78 negative triangles 220: dt=0.7660, 80 negative triangles 221: dt=0.7660, 78 negative triangles 222: dt=0.7660, 76 negative triangles 223: dt=0.7660, 77 negative triangles 224: dt=0.7660, 81 negative triangles 225: dt=0.7660, 79 negative triangles 226: dt=0.7660, 77 negative triangles 227: dt=0.7660, 76 negative triangles 228: dt=0.7660, 77 negative triangles 229: dt=0.7660, 77 negative triangles 230: dt=0.7660, 79 negative triangles 231: dt=0.7660, 78 negative triangles 232: dt=0.7277, 77 negative triangles 233: dt=0.7277, 77 negative triangles 234: dt=0.7277, 74 negative triangles 235: dt=0.7277, 76 negative triangles 236: dt=0.7277, 76 negative triangles 237: dt=0.7277, 73 negative triangles 238: dt=0.7277, 73 negative triangles 239: dt=0.7277, 76 negative triangles 240: dt=0.7277, 76 negative triangles 241: dt=0.7277, 75 negative triangles 242: dt=0.7277, 78 negative triangles 243: dt=0.7277, 76 negative triangles 244: dt=0.7277, 76 negative triangles 245: dt=0.7277, 72 negative triangles 246: dt=0.7277, 71 negative triangles 247: dt=0.7277, 72 negative triangles 248: dt=0.7277, 73 negative triangles 249: dt=0.7277, 73 negative triangles 250: dt=0.7277, 73 negative triangles 251: dt=0.7277, 73 negative triangles 252: dt=0.7277, 73 negative triangles 253: dt=0.7277, 71 negative triangles 254: dt=0.7277, 70 negative triangles 255: dt=0.7277, 71 negative triangles 256: dt=0.7277, 71 negative triangles 257: dt=0.7277, 72 negative triangles 258: dt=0.7277, 71 negative triangles 259: dt=0.7277, 69 negative triangles 260: dt=0.7277, 69 negative triangles 261: dt=0.7277, 72 negative triangles 262: dt=0.7277, 71 negative triangles 263: dt=0.7277, 72 negative triangles 264: dt=0.7277, 70 negative triangles 265: dt=0.7277, 68 negative triangles 266: dt=0.7277, 67 negative triangles 267: dt=0.7277, 66 negative triangles 268: dt=0.7277, 67 negative triangles 269: dt=0.7277, 68 negative triangles 270: dt=0.7277, 68 negative triangles 271: dt=0.7277, 66 negative triangles 272: dt=0.7277, 66 negative triangles 273: dt=0.7277, 67 negative triangles 274: dt=0.7277, 69 negative triangles 275: dt=0.7277, 70 negative triangles 276: dt=0.7277, 70 negative triangles 277: dt=0.6914, 66 negative triangles 278: dt=0.6914, 66 negative triangles 279: dt=0.6914, 69 negative triangles 280: dt=0.6914, 68 negative triangles 281: dt=0.6914, 65 negative triangles 282: dt=0.6914, 65 negative triangles 283: dt=0.6914, 66 negative triangles 284: dt=0.6914, 66 negative triangles 285: dt=0.6914, 66 negative triangles 286: dt=0.6914, 67 negative triangles 287: dt=0.6914, 63 negative triangles 288: dt=0.6914, 63 negative triangles 289: dt=0.6914, 61 negative triangles 290: dt=0.6914, 59 negative triangles 291: dt=0.6914, 60 negative triangles 292: dt=0.6914, 60 negative triangles 293: dt=0.6914, 59 negative triangles 294: dt=0.6914, 59 negative triangles 295: dt=0.6914, 58 negative triangles 296: dt=0.6914, 58 negative triangles 297: dt=0.6914, 57 negative triangles 298: dt=0.6914, 56 negative triangles 299: dt=0.6914, 56 negative triangles 300: dt=0.6914, 56 negative triangles 301: dt=0.6914, 56 negative triangles 302: dt=0.6914, 56 negative triangles 303: dt=0.6914, 57 negative triangles 304: dt=0.6914, 56 negative triangles 305: dt=0.6914, 59 negative triangles 306: dt=0.6914, 60 negative triangles 307: dt=0.6914, 56 negative triangles 308: dt=0.6914, 55 negative triangles 309: dt=0.6914, 55 negative triangles 310: dt=0.6914, 53 negative triangles 311: dt=0.6914, 54 negative triangles 312: dt=0.6914, 54 negative triangles 313: dt=0.6914, 54 negative triangles 314: dt=0.6914, 52 negative triangles 315: dt=0.6914, 52 negative triangles 316: dt=0.6914, 54 negative triangles 317: dt=0.6914, 54 negative triangles 318: dt=0.6914, 56 negative triangles 319: dt=0.6914, 53 negative triangles 320: dt=0.6914, 53 negative triangles 321: dt=0.6914, 53 negative triangles 322: dt=0.6914, 51 negative triangles 323: dt=0.6914, 50 negative triangles 324: dt=0.6914, 52 negative triangles 325: dt=0.6914, 49 negative triangles 326: dt=0.6914, 49 negative triangles 327: dt=0.6914, 50 negative triangles 328: dt=0.6914, 50 negative triangles 329: dt=0.6914, 49 negative triangles 330: dt=0.6914, 48 negative triangles 331: dt=0.6914, 49 negative triangles 332: dt=0.6914, 51 negative triangles 333: dt=0.6914, 48 negative triangles 334: dt=0.6914, 46 negative triangles 335: dt=0.6914, 46 negative triangles 336: dt=0.6914, 44 negative triangles 337: dt=0.6914, 45 negative triangles 338: dt=0.6914, 48 negative triangles 339: dt=0.6914, 44 negative triangles 340: dt=0.6914, 45 negative triangles 341: dt=0.6914, 46 negative triangles 342: dt=0.6914, 45 negative triangles 343: dt=0.6914, 44 negative triangles 344: dt=0.6914, 44 negative triangles 345: dt=0.6914, 42 negative triangles 346: dt=0.6914, 43 negative triangles 347: dt=0.6914, 43 negative triangles 348: dt=0.6914, 41 negative triangles 349: dt=0.6914, 39 negative triangles 350: dt=0.6914, 38 negative triangles 351: dt=0.6914, 36 negative triangles 352: dt=0.6914, 35 negative triangles 353: dt=0.6914, 37 negative triangles 354: dt=0.6914, 36 negative triangles 355: dt=0.6914, 33 negative triangles 356: dt=0.6914, 34 negative triangles 357: dt=0.6914, 33 negative triangles 358: dt=0.6914, 32 negative triangles 359: dt=0.6914, 34 negative triangles 360: dt=0.6914, 32 negative triangles 361: dt=0.6914, 30 negative triangles 362: dt=0.6914, 30 negative triangles 363: dt=0.6914, 32 negative triangles 364: dt=0.6914, 30 negative triangles 365: dt=0.6914, 28 negative triangles 366: dt=0.6914, 25 negative triangles 367: dt=0.6914, 26 negative triangles 368: dt=0.6914, 23 negative triangles 369: dt=0.6914, 23 negative triangles 370: dt=0.6914, 22 negative triangles 371: dt=0.6914, 20 negative triangles 372: dt=0.6914, 20 negative triangles 373: dt=0.6914, 21 negative triangles 374: dt=0.6914, 19 negative triangles 375: dt=0.6914, 20 negative triangles 376: dt=0.6914, 19 negative triangles 377: dt=0.6914, 18 negative triangles 378: dt=0.6914, 16 negative triangles 379: dt=0.6914, 15 negative triangles 380: dt=0.6914, 11 negative triangles 381: dt=0.6914, 13 negative triangles 382: dt=0.6914, 11 negative triangles 383: dt=0.6914, 11 negative triangles 384: dt=0.6914, 10 negative triangles 385: dt=0.6914, 10 negative triangles 386: dt=0.6914, 9 negative triangles 387: dt=0.6914, 10 negative triangles 388: dt=0.6914, 8 negative triangles 389: dt=0.6914, 9 negative triangles 390: dt=0.6914, 8 negative triangles 391: dt=0.6914, 9 negative triangles 392: dt=0.6914, 6 negative triangles 393: dt=0.6914, 7 negative triangles 394: dt=0.6914, 6 negative triangles 395: dt=0.6914, 7 negative triangles 396: dt=0.6914, 4 negative triangles 397: dt=0.6914, 5 negative triangles 398: dt=0.6914, 3 negative triangles 399: dt=0.6914, 4 negative triangles 400: dt=0.6914, 3 negative triangles 401: dt=0.6914, 2 negative triangles 402: dt=0.6914, 3 negative triangles 403: dt=0.6914, 1 negative triangles 404: dt=0.6914, 1 negative triangles 405: dt=0.6914, 2 negative triangles 406: dt=0.6914, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.58 hours mris_register utimesec 5771.348621 mris_register stimesec 1.895711 mris_register ru_maxrss 260232 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 37602 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5584 mris_register ru_oublock 9488 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 153275 mris_register ru_nivcsw 10939 FSRUNTIME@ mris_register 0.5822 hours 1 threads PIDs (18744 18747) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Wed Jan 18 23:13:56 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Wed Jan 18 23:13:56 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 27793 of (27793 27796) to complete... Waiting for PID 27796 of (27793 27796) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (27793 27796) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Wed Jan 18 23:13:58 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mrisp_paint -a 5 /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Wed Jan 18 23:13:58 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mrisp_paint -a 5 /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 27852 of (27852 27855) to complete... Waiting for PID 27855 of (27852 27855) to complete... mrisp_paint -a 5 /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (27852 27855) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Wed Jan 18 23:13:59 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Wed Jan 18 23:13:59 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 27901 of (27901 27904) to complete... Waiting for PID 27904 of (27901 27904) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1529 labels changed using aseg relabeling using gibbs priors... 000: 2951 changed, 133349 examined... 001: 690 changed, 12528 examined... 002: 135 changed, 3921 examined... 003: 48 changed, 830 examined... 004: 15 changed, 286 examined... 005: 6 changed, 98 examined... 006: 1 changed, 37 examined... 007: 0 changed, 6 examined... 206 labels changed using aseg 000: 105 total segments, 61 labels (180 vertices) changed 001: 45 total segments, 1 labels (2 vertices) changed 002: 43 total segments, 4 labels (11 vertices) changed 003: 39 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... 1547 vertices marked for relabeling... 1547 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1240 labels changed using aseg relabeling using gibbs priors... 000: 2650 changed, 133018 examined... 001: 633 changed, 11348 examined... 002: 134 changed, 3608 examined... 003: 48 changed, 860 examined... 004: 17 changed, 313 examined... 005: 7 changed, 114 examined... 006: 4 changed, 42 examined... 007: 3 changed, 20 examined... 008: 0 changed, 14 examined... 154 labels changed using aseg 000: 94 total segments, 53 labels (289 vertices) changed 001: 42 total segments, 1 labels (1 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1131 vertices marked for relabeling... 1131 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 12 seconds. PIDs (27901 27904) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Wed Jan 18 23:14:11 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs bert lh #-------------------------------------------- #@# Make Pial Surf rh Wed Jan 18 23:14:11 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs bert rh Waiting for PID 28006 of (28006 28009) to complete... Waiting for PID 28009 of (28006 28009) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs bert lh using white.preaparc starting white location... using white.preaparc 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 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... 21017 bright wm thresholded. 10805 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.orig... computing class statistics... border white: 257825 voxels (1.54%) border gray 278292 voxels (1.66%) WM (103.0): 103.1 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.0 +- 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+-3.5, GM=82+-7.0 mean inside = 100.0, mean outside = 88.0 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.05-->4.51) (max @ vno 82239 --> 132883) face area 0.33 +- 0.15 (0.00-->3.35) mean absolute distance = 0.83 +- 1.03 2537 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 3 with 65 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 5 with 48 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown mean border=89.4, 64 (64) missing vertices, mean dist 0.5 [1.4 (%12.3)->0.8 (%87.7))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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 (0.03-->4.71) (max @ vno 82239 --> 132883) face area 0.33 +- 0.16 (0.00-->3.38) mean absolute distance = 0.46 +- 0.72 4387 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1710190.0, rms=6.517 001: dt: 0.5000, sse=1059440.0, rms=4.104 (37.023%) 002: dt: 0.5000, sse=816159.0, rms=2.703 (34.147%) 003: dt: 0.5000, sse=737128.5, rms=2.043 (24.416%) 004: dt: 0.5000, sse=708045.9, rms=1.735 (15.067%) 005: dt: 0.5000, sse=699220.2, rms=1.620 (6.646%) 006: dt: 0.5000, sse=694557.8, rms=1.559 (3.729%) rms = 1.55, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=694204.2, rms=1.552 (0.437%) 008: dt: 0.2500, sse=675718.4, rms=1.189 (23.383%) rms = 1.15, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=673545.7, rms=1.146 (3.610%) rms = 1.13, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=672841.0, rms=1.133 (1.152%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 34 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 36 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown mean border=91.9, 45 (14) missing vertices, mean dist -0.3 [0.6 (%71.7)->0.2 (%28.3))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=terri, 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 (0.05-->4.87) (max @ vno 82239 --> 132883) face area 0.36 +- 0.17 (0.00-->4.13) mean absolute distance = 0.33 +- 0.46 3888 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1039871.8, rms=3.672 011: dt: 0.5000, sse=825184.4, rms=2.264 (38.348%) 012: dt: 0.5000, sse=765505.3, rms=1.691 (25.283%) 013: dt: 0.5000, sse=746211.9, rms=1.452 (14.144%) 014: dt: 0.5000, sse=738662.3, rms=1.372 (5.483%) rms = 1.39, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=729230.1, rms=1.175 (14.373%) 016: dt: 0.2500, sse=724568.4, rms=1.075 (8.527%) rms = 1.04, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=722896.2, rms=1.045 (2.823%) rms = 1.03, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=722020.2, rms=1.029 (1.518%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 35 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 42 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown mean border=94.0, 46 (12) missing vertices, mean dist -0.2 [0.4 (%73.3)->0.2 (%26.7))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=terri, 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 (0.10-->4.94) (max @ vno 82239 --> 132883) face area 0.35 +- 0.16 (0.00-->4.16) mean absolute distance = 0.25 +- 0.34 3847 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=869608.2, rms=2.873 019: dt: 0.5000, sse=724810.6, rms=1.552 (45.973%) 020: dt: 0.5000, sse=699594.4, rms=1.218 (21.544%) 021: dt: 0.5000, sse=696063.9, rms=1.153 (5.316%) rms = 1.18, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=686957.6, rms=0.982 (14.883%) 023: dt: 0.2500, sse=683588.7, rms=0.908 (7.522%) rms = 0.90, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=683201.9, rms=0.903 (0.571%) rms = 0.90, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=682496.0, rms=0.895 (0.821%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 34 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 4 with 58 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown mean border=94.6, 62 (10) missing vertices, mean dist -0.1 [0.3 (%58.2)->0.2 (%41.8))] %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=terri, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=688365.5, rms=1.299 026: dt: 0.5000, sse=662462.5, rms=0.785 (39.559%) rms = 0.95, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=659493.6, rms=0.717 (8.635%) rms = 0.72, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=659010.7, rms=0.715 (0.310%) rms = 0.71, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=661535.6, rms=0.710 (0.742%) positioning took 0.4 minutes generating cortex label... 5 non-cortical segments detected only using segment with 8344 vertices erasing segment 1 (vno[0] = 94669) erasing segment 2 (vno[0] = 97383) erasing segment 3 (vno[0] = 101538) erasing segment 4 (vno[0] = 133140) writing cortex label to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label... writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.area vertex spacing 0.89 +- 0.26 (0.04-->5.00) (max @ vno 82239 --> 132883) face area 0.34 +- 0.16 (0.00-->4.14) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=69.9, 64 (64) missing vertices, mean dist 1.9 [0.5 (%0.0)->2.9 (%100.0))] %17 local maxima, %44 large gradients and %33 min vals, 288 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=terri, 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=17034442.0, rms=25.493 001: dt: 0.0500, sse=15566591.0, rms=24.325 (4.579%) 002: dt: 0.0500, sse=14501211.0, rms=23.442 (3.634%) 003: dt: 0.0500, sse=13673172.0, rms=22.731 (3.032%) 004: dt: 0.0500, sse=12994062.0, rms=22.131 (2.640%) 005: dt: 0.0500, sse=12415103.0, rms=21.606 (2.372%) 006: dt: 0.0500, sse=11907119.0, rms=21.134 (2.182%) 007: dt: 0.0500, sse=11451267.0, rms=20.702 (2.045%) 008: dt: 0.0500, sse=11036520.0, rms=20.301 (1.938%) 009: dt: 0.0500, sse=10653990.0, rms=19.924 (1.859%) 010: dt: 0.0500, sse=10298805.0, rms=19.567 (1.792%) positioning took 0.8 minutes mean border=69.7, 59 (35) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.4 (%100.0))] %18 local maxima, %44 large gradients and %32 min vals, 262 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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=10979712.0, rms=20.245 011: dt: 0.0500, sse=10645765.0, rms=19.915 (1.630%) 012: dt: 0.0500, sse=10331690.0, rms=19.599 (1.584%) 013: dt: 0.0500, sse=10034998.0, rms=19.296 (1.545%) 014: dt: 0.0500, sse=9754328.0, rms=19.005 (1.508%) 015: dt: 0.0500, sse=9488453.0, rms=18.725 (1.473%) 016: dt: 0.0500, sse=9235941.0, rms=18.456 (1.441%) 017: dt: 0.0500, sse=8995863.0, rms=18.195 (1.411%) 018: dt: 0.0500, sse=8767315.0, rms=17.944 (1.382%) 019: dt: 0.0500, sse=8549791.0, rms=17.701 (1.353%) 020: dt: 0.0500, sse=8342338.5, rms=17.466 (1.326%) positioning took 0.8 minutes mean border=69.5, 60 (26) missing vertices, mean dist 1.4 [0.1 (%0.3)->2.0 (%99.7))] %19 local maxima, %44 large gradients and %31 min vals, 251 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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=8458598.0, rms=17.603 021: dt: 0.0500, sse=8256831.0, rms=17.373 (1.304%) 022: dt: 0.0500, sse=8064216.0, rms=17.151 (1.278%) 023: dt: 0.0500, sse=7879439.5, rms=16.935 (1.259%) 024: dt: 0.0500, sse=7702813.5, rms=16.726 (1.234%) 025: dt: 0.0500, sse=7533266.5, rms=16.523 (1.215%) 026: dt: 0.0500, sse=7370897.5, rms=16.326 (1.193%) 027: dt: 0.0500, sse=7214160.5, rms=16.133 (1.180%) 028: dt: 0.0500, sse=7062943.5, rms=15.945 (1.166%) 029: dt: 0.0500, sse=6916214.0, rms=15.760 (1.159%) 030: dt: 0.0500, sse=6774154.5, rms=15.579 (1.149%) positioning took 0.8 minutes mean border=69.4, 86 (24) missing vertices, mean dist 1.1 [0.1 (%3.8)->1.8 (%96.2))] %19 local maxima, %45 large gradients and %31 min vals, 252 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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=6844965.0, rms=15.669 031: dt: 0.5000, sse=5817075.5, rms=14.299 (8.747%) 032: dt: 0.5000, sse=4980390.5, rms=13.073 (8.574%) 033: dt: 0.5000, sse=4225607.0, rms=11.861 (9.267%) 034: dt: 0.5000, sse=3515723.8, rms=10.593 (10.693%) 035: dt: 0.5000, sse=2860189.2, rms=9.271 (12.475%) 036: dt: 0.5000, sse=2291616.2, rms=7.946 (14.292%) 037: dt: 0.5000, sse=1843907.0, rms=6.727 (15.340%) 038: dt: 0.5000, sse=1542195.4, rms=5.756 (14.440%) 039: dt: 0.5000, sse=1354442.1, rms=5.064 (12.025%) 040: dt: 0.5000, sse=1250681.0, rms=4.629 (8.582%) 041: dt: 0.5000, sse=1188988.4, rms=4.358 (5.869%) 042: dt: 0.5000, sse=1155927.4, rms=4.197 (3.679%) 043: dt: 0.5000, sse=1136143.9, rms=4.105 (2.198%) 044: dt: 0.5000, sse=1125660.2, rms=4.049 (1.365%) rms = 4.02, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1118170.8, rms=4.016 (0.808%) 046: dt: 0.2500, sse=1012437.9, rms=3.377 (15.911%) 047: dt: 0.2500, sse=984042.9, rms=3.202 (5.183%) rms = 3.20, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=984350.7, rms=3.199 (0.107%) 049: dt: 0.1250, sse=969717.9, rms=3.101 (3.069%) rms = 3.09, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=968093.6, rms=3.090 (0.337%) positioning took 2.0 minutes mean border=68.3, 1802 (10) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.4 (%56.0))] %36 local maxima, %31 large gradients and %27 min vals, 164 gradients ignored tol=1.0e-04, sigma=1.0, host=terri, 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=1234046.9, rms=3.733 051: dt: 0.5000, sse=1172967.9, rms=3.402 (8.854%) 052: dt: 0.5000, sse=1156188.4, rms=3.334 (2.002%) rms = 3.46, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1060930.0, rms=2.640 (20.807%) 054: dt: 0.2500, sse=1031155.8, rms=2.384 (9.721%) rms = 2.34, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1026465.1, rms=2.342 (1.761%) 056: dt: 0.1250, sse=1010500.8, rms=2.190 (6.462%) rms = 2.17, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1007990.6, rms=2.169 (0.981%) positioning took 1.0 minutes mean border=67.7, 1932 (10) missing vertices, mean dist 0.1 [0.1 (%45.2)->0.3 (%54.8))] %48 local maxima, %19 large gradients and %25 min vals, 145 gradients ignored tol=1.0e-04, sigma=0.5, host=terri, 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=1037078.9, rms=2.462 rms = 2.71, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1013176.7, rms=2.251 (8.565%) 059: dt: 0.2500, sse=1004205.4, rms=2.171 (3.536%) rms = 2.16, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1002165.4, rms=2.161 (0.459%) 061: dt: 0.1250, sse=995771.7, rms=2.096 (3.015%) rms = 2.09, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=994315.5, rms=2.086 (0.510%) positioning took 0.8 minutes mean border=67.2, 3445 (10) missing vertices, mean dist 0.0 [0.1 (%48.0)->0.2 (%52.0))] %52 local maxima, %16 large gradients and %25 min vals, 147 gradients ignored tol=1.0e-04, sigma=0.2, host=terri, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1003252.8, rms=2.172 rms = 2.41, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=993601.3, rms=2.077 (4.374%) rms = 2.05, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=989159.9, rms=2.046 (1.510%) rms = 2.00, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=985344.5, rms=2.004 (2.038%) positioning took 0.5 minutes writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.08-->6.37) (max @ vno 89251 --> 89270) face area 0.40 +- 0.31 (0.00-->6.20) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133349 vertices processed 25000 of 133349 vertices processed 50000 of 133349 vertices processed 75000 of 133349 vertices processed 100000 of 133349 vertices processed 125000 of 133349 vertices processed 0 of 133349 vertices processed 25000 of 133349 vertices processed 50000 of 133349 vertices processed 75000 of 133349 vertices processed 100000 of 133349 vertices processed 125000 of 133349 vertices processed thickness calculation complete, 195:542 truncations. 33998 vertices at 0 distance 98062 vertices at 1 distance 75418 vertices at 2 distance 30287 vertices at 3 distance 9758 vertices at 4 distance 3121 vertices at 5 distance 1139 vertices at 6 distance 372 vertices at 7 distance 123 vertices at 8 distance 44 vertices at 9 distance 36 vertices at 10 distance 27 vertices at 11 distance 23 vertices at 12 distance 12 vertices at 13 distance 9 vertices at 14 distance 8 vertices at 15 distance 6 vertices at 16 distance 4 vertices at 17 distance 1 vertices at 18 distance 1 vertices at 19 distance 3 vertices at 20 distance writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.thickness positioning took 12.3 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs bert rh using white.preaparc starting white location... using white.preaparc 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 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... 21017 bright wm thresholded. 10805 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.orig... computing class statistics... border white: 257825 voxels (1.54%) border gray 278292 voxels (1.66%) WM (103.0): 103.1 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.0 +- 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 = 100.2, mean outside = 88.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.04-->7.95) (max @ vno 74265 --> 132724) face area 0.33 +- 0.15 (0.00-->5.32) mean absolute distance = 0.83 +- 1.02 2585 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 38 points - only 0.00% unknown deleting segment 3 with 27 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown mean border=89.8, 41 (41) missing vertices, mean dist 0.5 [1.4 (%12.4)->0.8 (%87.6))] %56 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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 (0.10-->8.09) (max @ vno 132724 --> 74265) face area 0.33 +- 0.16 (0.00-->5.02) mean absolute distance = 0.46 +- 0.70 3713 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1666061.6, rms=6.374 001: dt: 0.5000, sse=1026346.4, rms=3.927 (38.399%) 002: dt: 0.5000, sse=797698.8, rms=2.529 (35.583%) 003: dt: 0.5000, sse=726340.6, rms=1.902 (24.801%) 004: dt: 0.5000, sse=701142.6, rms=1.613 (15.195%) 005: dt: 0.5000, sse=693853.0, rms=1.504 (6.787%) 006: dt: 0.5000, sse=689693.6, rms=1.447 (3.729%) rms = 1.44, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=691496.9, rms=1.444 (0.263%) 008: dt: 0.2500, sse=674194.3, rms=1.113 (22.938%) rms = 1.07, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=672456.8, rms=1.075 (3.397%) rms = 1.07, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=671963.2, rms=1.066 (0.802%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 46 points - only 0.00% unknown deleting segment 1 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown mean border=92.3, 31 (6) missing vertices, mean dist -0.3 [0.5 (%71.5)->0.2 (%28.5))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=terri, 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 (0.06-->8.04) (max @ vno 132724 --> 74265) face area 0.36 +- 0.17 (0.00-->6.30) mean absolute distance = 0.33 +- 0.44 4495 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1026526.2, rms=3.616 011: dt: 0.5000, sse=816163.8, rms=2.208 (38.955%) 012: dt: 0.5000, sse=758322.7, rms=1.634 (25.961%) 013: dt: 0.5000, sse=743187.8, rms=1.391 (14.864%) 014: dt: 0.5000, sse=732932.9, rms=1.295 (6.966%) rms = 1.30, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=723388.1, rms=1.105 (14.673%) 016: dt: 0.2500, sse=718881.2, rms=1.009 (8.666%) rms = 0.99, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=717885.0, rms=0.989 (1.981%) rms = 0.98, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=717462.2, rms=0.976 (1.322%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 34 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown mean border=94.3, 31 (4) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.2 (%26.6))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=terri, 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 (0.09-->8.14) (max @ vno 132724 --> 74265) face area 0.35 +- 0.17 (0.00-->6.49) mean absolute distance = 0.24 +- 0.33 3695 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=858018.1, rms=2.795 019: dt: 0.5000, sse=717951.8, rms=1.474 (47.253%) 020: dt: 0.5000, sse=694796.6, rms=1.158 (21.487%) 021: dt: 0.5000, sse=690701.6, rms=1.103 (4.689%) rms = 1.13, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=684957.6, rms=0.946 (14.258%) 023: dt: 0.2500, sse=681439.8, rms=0.883 (6.633%) rms = 0.88, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=681039.4, rms=0.882 (0.133%) rms = 0.88, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=682766.1, rms=0.877 (0.625%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 29 points - only 0.00% unknown deleting segment 1 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown mean border=94.9, 36 (4) missing vertices, mean dist -0.1 [0.3 (%57.7)->0.2 (%42.3))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=terri, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=687012.9, rms=1.244 026: dt: 0.5000, sse=663678.6, rms=0.765 (38.497%) rms = 0.93, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=659165.0, rms=0.708 (7.392%) rms = 0.71, time step reduction 2 of 3 to 0.125... rms = 0.70, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=658399.2, rms=0.704 (0.567%) positioning took 0.4 minutes generating cortex label... 7 non-cortical segments detected only using segment with 8127 vertices erasing segment 1 (vno[0] = 70860) erasing segment 2 (vno[0] = 83698) erasing segment 3 (vno[0] = 94129) erasing segment 4 (vno[0] = 97576) erasing segment 5 (vno[0] = 98272) erasing segment 6 (vno[0] = 104770) writing cortex label to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label... writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.area vertex spacing 0.90 +- 0.26 (0.07-->8.05) (max @ vno 74265 --> 132724) face area 0.34 +- 0.16 (0.00-->6.13) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 10 points - only 0.00% unknown deleting segment 2 with 28 points - only 0.00% unknown removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=70.9, 35 (35) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.9 (%100.0))] %18 local maxima, %46 large gradients and %31 min vals, 311 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=terri, 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=16128520.0, rms=24.798 001: dt: 0.0500, sse=14734922.0, rms=23.656 (4.603%) 002: dt: 0.0500, sse=13719176.0, rms=22.788 (3.670%) 003: dt: 0.0500, sse=12928609.0, rms=22.089 (3.070%) 004: dt: 0.0500, sse=12279243.0, rms=21.497 (2.679%) 005: dt: 0.0500, sse=11725339.0, rms=20.979 (2.409%) 006: dt: 0.0500, sse=11239093.0, rms=20.513 (2.219%) 007: dt: 0.0500, sse=10803386.0, rms=20.087 (2.079%) 008: dt: 0.0500, sse=10407175.0, rms=19.691 (1.970%) 009: dt: 0.0500, sse=10043010.0, rms=19.320 (1.884%) 010: dt: 0.0500, sse=9705172.0, rms=18.969 (1.815%) positioning took 0.8 minutes mean border=70.7, 30 (14) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.3 (%100.0))] %19 local maxima, %46 large gradients and %30 min vals, 294 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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=10357120.0, rms=19.641 011: dt: 0.0500, sse=10039621.0, rms=19.317 (1.649%) 012: dt: 0.0500, sse=9741618.0, rms=19.008 (1.600%) 013: dt: 0.0500, sse=9460669.0, rms=18.712 (1.558%) 014: dt: 0.0500, sse=9195330.0, rms=18.428 (1.519%) 015: dt: 0.0500, sse=8944253.0, rms=18.155 (1.482%) 016: dt: 0.0500, sse=8706305.0, rms=17.892 (1.447%) 017: dt: 0.0500, sse=8480430.0, rms=17.639 (1.415%) 018: dt: 0.0500, sse=8265745.0, rms=17.395 (1.384%) 019: dt: 0.0500, sse=8061453.5, rms=17.159 (1.354%) 020: dt: 0.0500, sse=7866860.5, rms=16.932 (1.326%) positioning took 0.7 minutes mean border=70.5, 39 (11) missing vertices, mean dist 1.4 [0.1 (%0.3)->2.0 (%99.7))] %19 local maxima, %46 large gradients and %29 min vals, 283 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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=7963120.5, rms=17.050 021: dt: 0.0500, sse=7774068.5, rms=16.827 (1.305%) 022: dt: 0.0500, sse=7593684.0, rms=16.612 (1.279%) 023: dt: 0.0500, sse=7421009.0, rms=16.403 (1.256%) 024: dt: 0.0500, sse=7256125.0, rms=16.201 (1.231%) 025: dt: 0.0500, sse=7098401.0, rms=16.006 (1.207%) 026: dt: 0.0500, sse=6947251.5, rms=15.816 (1.186%) 027: dt: 0.0500, sse=6801580.0, rms=15.631 (1.171%) 028: dt: 0.0500, sse=6660480.0, rms=15.449 (1.162%) 029: dt: 0.0500, sse=6523755.0, rms=15.271 (1.153%) 030: dt: 0.0500, sse=6390817.0, rms=15.096 (1.147%) positioning took 0.8 minutes mean border=70.4, 74 (8) missing vertices, mean dist 1.1 [0.1 (%3.7)->1.7 (%96.3))] %20 local maxima, %46 large gradients and %29 min vals, 253 gradients ignored tol=1.0e-04, sigma=2.0, host=terri, 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=6457985.0, rms=15.185 031: dt: 0.5000, sse=5486919.0, rms=13.846 (8.820%) 032: dt: 0.5000, sse=4696129.0, rms=12.646 (8.665%) 033: dt: 0.5000, sse=3989233.2, rms=11.470 (9.301%) 034: dt: 0.5000, sse=3338501.0, rms=10.265 (10.499%) 035: dt: 0.5000, sse=2733030.0, rms=9.004 (12.286%) 036: dt: 0.5000, sse=2205528.5, rms=7.738 (14.067%) 037: dt: 0.5000, sse=1773525.9, rms=6.524 (15.682%) 038: dt: 0.5000, sse=1486103.8, rms=5.568 (14.661%) 039: dt: 0.5000, sse=1301937.9, rms=4.863 (12.657%) 040: dt: 0.5000, sse=1208628.4, rms=4.457 (8.352%) 041: dt: 0.5000, sse=1147358.1, rms=4.175 (6.318%) 042: dt: 0.5000, sse=1123223.0, rms=4.053 (2.925%) 043: dt: 0.5000, sse=1099566.2, rms=3.939 (2.807%) rms = 3.91, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=1094812.2, rms=3.911 (0.731%) 045: dt: 0.2500, sse=989220.9, rms=3.256 (16.745%) 046: dt: 0.2500, sse=963820.1, rms=3.092 (5.032%) rms = 3.08, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=962068.5, rms=3.076 (0.511%) 048: dt: 0.1250, sse=949741.1, rms=2.990 (2.812%) rms = 2.98, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=948046.4, rms=2.978 (0.388%) positioning took 1.9 minutes mean border=69.2, 1660 (3) missing vertices, mean dist 0.1 [0.2 (%42.1)->0.4 (%57.9))] %39 local maxima, %30 large gradients and %25 min vals, 110 gradients ignored tol=1.0e-04, sigma=1.0, host=terri, 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=1219847.0, rms=3.707 050: dt: 0.5000, sse=1140310.8, rms=3.251 (12.299%) 051: dt: 0.5000, sse=1121995.8, rms=3.174 (2.354%) rms = 3.31, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=1030060.1, rms=2.464 (22.385%) 053: dt: 0.2500, sse=1002132.8, rms=2.202 (10.608%) 054: dt: 0.2500, sse=996965.2, rms=2.152 (2.271%) rms = 2.11, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=992474.2, rms=2.112 (1.864%) 056: dt: 0.1250, sse=979986.2, rms=1.981 (6.208%) rms = 1.96, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=977708.8, rms=1.959 (1.096%) positioning took 1.0 minutes mean border=68.4, 1802 (3) missing vertices, mean dist 0.1 [0.1 (%43.7)->0.3 (%56.3))] %51 local maxima, %18 large gradients and %24 min vals, 115 gradients ignored tol=1.0e-04, sigma=0.5, host=terri, 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=1016316.9, rms=2.369 rms = 2.58, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=986266.8, rms=2.090 (11.773%) 059: dt: 0.2500, sse=974478.6, rms=1.972 (5.620%) rms = 1.95, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=971411.4, rms=1.951 (1.080%) 061: dt: 0.1250, sse=965470.7, rms=1.885 (3.408%) rms = 1.87, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=963719.8, rms=1.869 (0.820%) positioning took 0.8 minutes mean border=68.0, 3041 (3) missing vertices, mean dist 0.0 [0.2 (%47.3)->0.2 (%52.7))] %55 local maxima, %15 large gradients and %23 min vals, 102 gradients ignored tol=1.0e-04, sigma=0.2, host=terri, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=974173.6, rms=1.987 rms = 2.25, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=963520.9, rms=1.872 (5.792%) rms = 1.84, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=959230.3, rms=1.837 (1.880%) rms = 1.79, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=955601.1, rms=1.794 (2.335%) positioning took 0.5 minutes writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.area.pial vertex spacing 1.00 +- 0.43 (0.09-->6.91) (max @ vno 89670 --> 88661) face area 0.40 +- 0.30 (0.00-->8.17) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133018 vertices processed 25000 of 133018 vertices processed 50000 of 133018 vertices processed 75000 of 133018 vertices processed 100000 of 133018 vertices processed 125000 of 133018 vertices processed 0 of 133018 vertices processed 25000 of 133018 vertices processed 50000 of 133018 vertices processed 75000 of 133018 vertices processed 100000 of 133018 vertices processed 125000 of 133018 vertices processed thickness calculation complete, 297:495 truncations. 35008 vertices at 0 distance 98496 vertices at 1 distance 75736 vertices at 2 distance 29215 vertices at 3 distance 9261 vertices at 4 distance 2764 vertices at 5 distance 913 vertices at 6 distance 297 vertices at 7 distance 131 vertices at 8 distance 48 vertices at 9 distance 36 vertices at 10 distance 18 vertices at 11 distance 13 vertices at 12 distance 21 vertices at 13 distance 8 vertices at 14 distance 7 vertices at 15 distance 4 vertices at 16 distance 7 vertices at 17 distance 0 vertices at 18 distance 2 vertices at 19 distance 7 vertices at 20 distance writing curvature file /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.thickness positioning took 12.2 minutes PIDs (28006 28009) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Wed Jan 18 23:26:30 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 lh /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.volume masking with /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label Total face volume 250241 Total vertex volume 246969 (mask=0) #@# bert lh 246969 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed Jan 18 23:26:33 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 rh /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.volume masking with /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label Total face volume 248922 Total vertex volume 245189 (mask=0) #@# bert rh 245189 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 18 23:26:36 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri 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 SUBJECTS_DIR is /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects 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 = 63 writing volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/ribbon.mgz mris_volmask took 10.78 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Wed Jan 18 23:37:24 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts 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 lh white 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 lh pial #----------------------------------------- #@# Parcellation Stats rh Wed Jan 18 23:37:24 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts 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 rh white 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 rh pial Waiting for PID 1870 of (1870 1873 1876 1879) to complete... Waiting for PID 1873 of (1870 1873 1876 1879) to complete... Waiting for PID 1876 of (1870 1873 1876 1879) to complete... Waiting for PID 1879 of (1870 1873 1876 1879) to complete... 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 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 250241 Total vertex volume 246969 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1205 841 2398 2.796 0.426 0.117 0.021 11 0.9 bankssts 856 578 1542 2.731 0.474 0.120 0.012 11 0.4 caudalanteriorcingulate 2803 1863 5938 2.831 0.541 0.114 0.021 26 2.4 caudalmiddlefrontal 2620 1627 3031 1.825 0.492 0.142 0.033 39 3.6 cuneus 548 407 1716 3.280 0.595 0.120 0.026 4 0.6 entorhinal 4162 2889 8559 2.711 0.585 0.130 0.027 52 4.4 fusiform 5017 3490 10661 2.709 0.505 0.129 0.028 71 5.5 inferiorparietal 5028 3525 12413 3.001 0.613 0.137 0.032 69 6.6 inferiortemporal 1473 936 2240 2.123 0.763 0.119 0.025 21 1.3 isthmuscingulate 8055 5134 12857 2.309 0.579 0.139 0.034 104 10.9 lateraloccipital 3596 2517 8164 2.893 0.636 0.141 0.034 51 5.4 lateralorbitofrontal 4517 3007 5848 1.865 0.490 0.128 0.029 57 5.5 lingual 3193 2195 6487 2.547 0.793 0.122 0.035 54 4.9 medialorbitofrontal 4694 3218 11990 3.140 0.587 0.127 0.026 60 4.9 middletemporal 930 615 1696 2.512 0.587 0.072 0.012 4 0.4 parahippocampal 2087 1357 3737 2.551 0.628 0.102 0.025 14 2.1 paracentral 2309 1611 5416 2.968 0.514 0.116 0.020 21 1.8 parsopercularis 972 638 2430 3.142 0.536 0.124 0.024 13 0.9 parsorbitalis 2300 1526 4549 2.774 0.502 0.115 0.020 23 1.8 parstriangularis 1923 1280 1814 1.584 0.413 0.126 0.030 20 2.2 pericalcarine 5777 3660 9203 2.261 0.688 0.101 0.022 45 4.9 postcentral 1678 1155 3168 2.467 0.548 0.128 0.022 23 1.6 posteriorcingulate 7233 4509 14603 2.990 0.651 0.102 0.021 52 6.5 precentral 5555 3729 9442 2.450 0.540 0.122 0.025 59 5.4 precuneus 923 607 2216 3.161 0.534 0.130 0.027 13 1.0 rostralanteriorcingulate 8555 5750 16348 2.555 0.516 0.128 0.028 109 9.5 rostralmiddlefrontal 10411 7145 24212 3.014 0.579 0.118 0.024 99 10.2 superiorfrontal 7755 5137 13898 2.410 0.528 0.121 0.023 86 7.0 superiorparietal 6059 4126 13621 2.968 0.571 0.110 0.020 55 4.7 superiortemporal 6890 4689 14084 2.748 0.551 0.125 0.023 76 6.3 supramarginal 393 282 1066 2.605 0.703 0.173 0.061 11 1.0 frontalpole 637 464 2674 3.727 0.623 0.174 0.058 13 1.6 temporalpole 777 489 1262 2.460 0.545 0.133 0.022 9 0.7 transversetemporal 3571 2379 7648 3.183 0.672 0.098 0.021 28 3.1 insula 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 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 250241 Total vertex volume 246969 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1205 821 2398 2.796 0.426 0.121 0.025 13 1.3 bankssts 856 640 1542 2.731 0.474 0.106 0.021 21 0.6 caudalanteriorcingulate 2803 2236 5938 2.831 0.541 0.117 0.021 34 2.5 caudalmiddlefrontal 2620 1810 3031 1.825 0.492 0.132 0.028 52 3.5 cuneus 548 654 1716 3.280 0.595 0.174 0.029 7 0.9 entorhinal 4162 3377 8559 2.711 0.585 0.129 0.027 51 5.3 fusiform 5017 4268 10661 2.709 0.505 0.135 0.026 49 5.9 inferiorparietal 5028 4571 12413 3.001 0.613 0.151 0.037 75 8.1 inferiortemporal 1473 1155 2240 2.123 0.763 0.140 0.039 26 2.5 isthmuscingulate 8055 6030 12857 2.309 0.579 0.127 0.028 104 9.6 lateraloccipital 3596 3092 8164 2.893 0.636 0.157 0.039 56 6.4 lateralorbitofrontal 4517 3429 5848 1.865 0.490 0.129 0.031 53 6.4 lingual 3193 2828 6487 2.547 0.793 0.147 0.033 56 5.2 medialorbitofrontal 4694 4299 11990 3.140 0.587 0.139 0.027 68 5.9 middletemporal 930 773 1696 2.512 0.587 0.109 0.023 7 1.0 parahippocampal 2087 1517 3737 2.551 0.628 0.103 0.019 21 1.6 paracentral 2309 1956 5416 2.968 0.514 0.130 0.025 22 2.8 parsopercularis 972 898 2430 3.142 0.536 0.141 0.032 13 1.3 parsorbitalis 2300 1747 4549 2.774 0.502 0.125 0.024 42 2.3 parstriangularis 1923 1084 1814 1.584 0.413 0.108 0.028 34 2.2 pericalcarine 5777 4522 9203 2.261 0.688 0.114 0.020 46 5.0 postcentral 1678 1370 3168 2.467 0.548 0.136 0.027 26 2.1 posteriorcingulate 7233 5201 14603 2.990 0.651 0.102 0.021 62 6.5 precentral 5555 3968 9442 2.450 0.540 0.124 0.046 73 6.4 precuneus 923 825 2216 3.161 0.534 0.153 0.035 25 1.3 rostralanteriorcingulate 8555 6778 16348 2.555 0.516 0.134 0.025 109 10.0 rostralmiddlefrontal 10411 8534 24212 3.014 0.579 0.124 0.025 110 11.4 superiorfrontal 7755 6260 13898 2.410 0.528 0.129 0.025 81 8.1 superiorparietal 6059 4877 13621 2.968 0.571 0.123 0.025 69 6.8 superiortemporal 6890 5452 14084 2.748 0.551 0.126 0.024 71 7.3 supramarginal 393 499 1066 2.605 0.703 0.186 0.037 4 0.6 frontalpole 637 957 2674 3.727 0.623 0.214 0.042 10 1.4 temporalpole 777 568 1262 2.460 0.545 0.107 0.023 6 0.7 transversetemporal 3571 2255 7648 3.183 0.672 0.113 0.028 46 4.6 insula 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 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 248922 Total vertex volume 245189 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1092 754 1975 2.611 0.488 0.094 0.019 7 0.7 bankssts 1090 747 2313 2.582 0.651 0.136 0.020 16 0.9 caudalanteriorcingulate 2616 1748 5352 2.901 0.474 0.109 0.020 19 2.1 caudalmiddlefrontal 2390 1528 3004 1.857 0.513 0.138 0.034 33 3.5 cuneus 462 340 1711 3.508 0.553 0.128 0.032 4 0.7 entorhinal 3978 2822 7777 2.594 0.557 0.127 0.028 50 4.7 fusiform 6983 4842 14944 2.749 0.468 0.127 0.025 86 7.1 inferiorparietal 4520 3163 11543 3.015 0.621 0.139 0.031 68 6.1 inferiortemporal 1210 788 2017 2.290 0.722 0.123 0.027 17 1.1 isthmuscingulate 8390 5525 12769 2.148 0.564 0.133 0.030 106 10.1 lateraloccipital 3842 2699 8648 2.964 0.665 0.131 0.034 52 5.1 lateralorbitofrontal 4372 2916 6273 2.024 0.556 0.134 0.032 57 6.1 lingual 3185 2236 6509 2.688 0.665 0.124 0.024 42 3.2 medialorbitofrontal 4861 3421 11976 2.944 0.572 0.130 0.029 67 5.6 middletemporal 1006 661 1879 2.610 0.623 0.083 0.017 7 0.5 parahippocampal 2337 1505 3914 2.510 0.509 0.109 0.023 19 2.1 paracentral 1938 1314 4088 2.936 0.453 0.120 0.024 18 1.8 parsopercularis 1387 917 3459 2.968 0.614 0.131 0.026 18 1.5 parsorbitalis 2615 1771 5335 2.673 0.477 0.119 0.022 29 2.2 parstriangularis 2024 1331 2044 1.746 0.551 0.115 0.025 16 2.0 pericalcarine 6174 3874 9569 2.243 0.682 0.100 0.019 48 4.8 postcentral 1742 1254 3485 2.540 0.578 0.139 0.025 24 1.9 posteriorcingulate 7578 4730 14786 2.851 0.646 0.106 0.022 56 7.3 precentral 5679 3862 10003 2.509 0.488 0.116 0.022 53 5.3 precuneus 964 649 2350 3.025 0.535 0.140 0.025 15 1.0 rostralanteriorcingulate 8456 5662 16992 2.628 0.502 0.129 0.029 100 9.7 rostralmiddlefrontal 9178 6147 21269 3.079 0.548 0.118 0.025 84 9.1 superiorfrontal 8088 5289 14312 2.415 0.522 0.117 0.023 87 7.0 superiorparietal 5224 3500 11651 2.992 0.547 0.106 0.020 47 4.3 superiortemporal 5475 3761 11230 2.776 0.512 0.121 0.023 58 5.3 supramarginal 497 333 1141 2.663 0.437 0.132 0.028 7 0.5 frontalpole 506 370 2146 3.955 0.446 0.160 0.040 8 0.8 temporalpole 554 327 819 2.346 0.484 0.115 0.022 5 0.4 transversetemporal 3766 2552 7868 3.174 0.737 0.109 0.023 33 3.4 insula 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 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 248922 Total vertex volume 245189 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1092 748 1975 2.611 0.488 0.120 0.025 13 1.2 bankssts 1090 971 2313 2.582 0.651 0.163 0.035 54 1.5 caudalanteriorcingulate 2616 1829 5352 2.901 0.474 0.111 0.023 66 2.7 caudalmiddlefrontal 2390 1801 3004 1.857 0.513 0.127 0.028 29 3.0 cuneus 462 616 1711 3.508 0.553 0.157 0.023 3 0.6 entorhinal 3978 3191 7777 2.594 0.557 0.142 0.033 54 6.1 fusiform 6983 5839 14944 2.749 0.468 0.132 0.025 70 7.6 inferiorparietal 4520 4324 11543 3.015 0.621 0.149 0.030 63 6.2 inferiortemporal 1210 923 2017 2.290 0.722 0.137 0.037 19 2.0 isthmuscingulate 8390 6363 12769 2.148 0.564 0.129 0.027 112 10.2 lateraloccipital 3842 3174 8648 2.964 0.665 0.148 0.039 65 6.1 lateralorbitofrontal 4372 3309 6273 2.024 0.556 0.127 0.033 50 6.0 lingual 3185 2694 6509 2.688 0.665 0.135 0.027 37 3.7 medialorbitofrontal 4861 4555 11976 2.944 0.572 0.144 0.028 56 6.0 middletemporal 1006 775 1879 2.610 0.623 0.111 0.021 57 0.9 parahippocampal 2337 1597 3914 2.510 0.509 0.107 0.021 32 2.0 paracentral 1938 1435 4088 2.936 0.453 0.116 0.025 20 2.2 parsopercularis 1387 1354 3459 2.968 0.614 0.147 0.027 14 1.8 parsorbitalis 2615 2182 5335 2.673 0.477 0.124 0.020 24 2.3 parstriangularis 2024 1147 2044 1.746 0.551 0.101 0.025 22 2.1 pericalcarine 6174 4603 9569 2.243 0.682 0.109 0.020 46 5.3 postcentral 1742 1430 3485 2.540 0.578 0.131 0.025 27 2.0 posteriorcingulate 7578 5452 14786 2.851 0.646 0.096 0.018 70 5.7 precentral 5679 4131 10003 2.509 0.488 0.121 0.024 69 6.1 precuneus 964 921 2350 3.025 0.535 0.160 0.034 27 1.4 rostralanteriorcingulate 8456 7006 16992 2.628 0.502 0.137 0.025 103 9.7 rostralmiddlefrontal 9178 7414 21269 3.079 0.548 0.125 0.025 98 9.5 superiorfrontal 8088 6290 14312 2.415 0.522 0.123 0.023 82 7.7 superiorparietal 5224 4273 11651 2.992 0.547 0.120 0.024 57 5.3 superiortemporal 5475 4151 11230 2.776 0.512 0.122 0.024 60 5.6 supramarginal 497 517 1141 2.663 0.437 0.165 0.024 6 0.5 frontalpole 506 696 2146 3.955 0.446 0.180 0.035 4 0.7 temporalpole 554 382 819 2.346 0.484 0.114 0.027 5 0.6 transversetemporal 3766 2289 7868 3.174 0.737 0.118 0.028 58 4.7 insula PIDs (1870 1873 1876 1879) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Wed Jan 18 23:38:02 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Wed Jan 18 23:38:02 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 2111 of (2111 2114) to complete... Waiting for PID 2114 of (2111 2114) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 83 labels changed using aseg relabeling using gibbs priors... 000: 8620 changed, 133349 examined... 001: 2064 changed, 33510 examined... 002: 614 changed, 10787 examined... 003: 281 changed, 3400 examined... 004: 140 changed, 1587 examined... 005: 74 changed, 783 examined... 006: 37 changed, 409 examined... 007: 19 changed, 187 examined... 008: 15 changed, 98 examined... 009: 3 changed, 78 examined... 010: 3 changed, 21 examined... 011: 4 changed, 18 examined... 012: 5 changed, 21 examined... 013: 2 changed, 21 examined... 014: 1 changed, 16 examined... 015: 0 changed, 7 examined... 27 labels changed using aseg 000: 245 total segments, 160 labels (2133 vertices) changed 001: 88 total segments, 5 labels (8 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1073 vertices marked for relabeling... 1073 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 33 labels changed using aseg relabeling using gibbs priors... 000: 8554 changed, 133018 examined... 001: 1818 changed, 33546 examined... 002: 521 changed, 9822 examined... 003: 220 changed, 2953 examined... 004: 90 changed, 1271 examined... 005: 48 changed, 517 examined... 006: 24 changed, 274 examined... 007: 18 changed, 144 examined... 008: 16 changed, 109 examined... 009: 5 changed, 85 examined... 010: 0 changed, 27 examined... 23 labels changed using aseg 000: 239 total segments, 154 labels (2306 vertices) changed 001: 96 total segments, 11 labels (53 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 23 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 803 vertices marked for relabeling... 803 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 15 seconds. PIDs (2111 2114) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jan 18 23:38:17 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts 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 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Wed Jan 18 23:38:17 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts 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 rh white Waiting for PID 2225 of (2225 2228) to complete... Waiting for PID 2228 of (2225 2228) to complete... 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 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 250241 Total vertex volume 246969 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1191 841 2298 2.524 0.471 0.136 0.029 15 1.4 G&S_frontomargin 1968 1310 3624 2.530 0.549 0.147 0.032 30 2.5 G&S_occipital_inf 1716 978 3119 2.613 0.639 0.103 0.023 15 1.5 G&S_paracentral 1419 951 3531 3.137 0.520 0.141 0.031 20 1.7 G&S_subcentral 930 612 2109 2.592 0.547 0.165 0.050 20 1.7 G&S_transv_frontopol 2320 1573 5034 2.962 0.449 0.117 0.022 24 2.1 G&S_cingul-Ant 1087 795 2084 2.698 0.467 0.106 0.012 7 0.6 G&S_cingul-Mid-Ant 1288 934 2481 2.580 0.454 0.107 0.018 10 0.9 G&S_cingul-Mid-Post 532 364 1399 2.910 0.439 0.158 0.035 9 0.7 G_cingul-Post-dorsal 303 189 557 2.309 0.676 0.138 0.030 6 0.4 G_cingul-Post-ventral 2461 1519 2921 1.742 0.451 0.147 0.036 38 3.8 G_cuneus 1260 881 3438 3.040 0.522 0.126 0.023 15 1.1 G_front_inf-Opercular 459 291 1251 2.997 0.358 0.133 0.025 9 0.4 G_front_inf-Orbital 1328 870 3240 2.927 0.491 0.126 0.024 19 1.2 G_front_inf-Triangul 4423 2935 10640 2.815 0.569 0.138 0.032 69 5.5 G_front_middle 7397 4936 19043 3.141 0.597 0.129 0.030 89 9.0 G_front_sup 716 465 1686 3.229 0.813 0.119 0.040 9 1.2 G_Ins_lg&S_cent_ins 766 495 2461 3.611 0.707 0.104 0.024 10 0.8 G_insular_short 2253 1474 4923 2.695 0.486 0.153 0.037 49 3.1 G_occipital_middle 1141 752 2275 2.484 0.522 0.107 0.020 9 0.8 G_occipital_sup 1706 1162 4089 2.842 0.604 0.147 0.030 29 2.1 G_oc-temp_lat-fusifor 3175 2053 4155 1.798 0.515 0.142 0.035 50 4.8 G_oc-temp_med-Lingual 1084 732 2797 2.930 0.715 0.101 0.023 9 1.0 G_oc-temp_med-Parahip 2166 1473 6140 3.173 0.635 0.145 0.035 37 3.3 G_orbital 1807 1228 4414 2.867 0.408 0.146 0.034 28 2.3 G_pariet_inf-Angular 3458 2337 8128 2.862 0.571 0.130 0.026 45 3.4 G_pariet_inf-Supramar 2954 1944 6257 2.562 0.574 0.131 0.027 45 2.8 G_parietal_sup 2097 1232 3585 2.299 0.579 0.102 0.026 18 2.3 G_postcentral 2810 1578 6758 3.220 0.692 0.102 0.024 25 2.9 G_precentral 2689 1774 5496 2.466 0.534 0.136 0.029 41 3.2 G_precuneus 1015 740 2487 2.378 0.663 0.151 0.064 32 3.2 G_rectus 570 401 1115 2.812 1.200 0.084 0.032 5 0.4 G_subcallosal 634 399 1232 2.640 0.608 0.150 0.026 10 0.6 G_temp_sup-G_T_transv 2159 1435 6285 3.206 0.553 0.138 0.030 32 2.5 G_temp_sup-Lateral 565 405 1738 3.570 0.570 0.103 0.030 4 0.7 G_temp_sup-Plan_polar 1117 752 2300 2.768 0.532 0.113 0.017 11 0.9 G_temp_sup-Plan_tempo 2810 1929 7944 3.122 0.583 0.153 0.040 53 4.6 G_temporal_inf 2572 1706 7499 3.223 0.542 0.139 0.033 44 3.4 G_temporal_middle 383 265 555 2.438 0.304 0.092 0.013 1 0.2 Lat_Fis-ant-Horizont 451 307 737 2.928 0.425 0.108 0.021 2 0.4 Lat_Fis-ant-Vertical 1277 851 1853 2.931 0.535 0.113 0.019 9 1.0 Lat_Fis-post 2244 1277 2841 1.989 0.560 0.135 0.041 28 3.7 Pole_occipital 1564 1141 5632 3.418 0.738 0.147 0.040 23 2.6 Pole_temporal 2572 1743 2751 1.811 0.556 0.117 0.024 23 2.3 S_calcarine 3055 2099 4020 2.184 0.717 0.090 0.015 12 2.0 S_central 1076 748 1570 2.376 0.446 0.087 0.013 4 0.5 S_cingul-Marginalis 533 352 877 2.941 0.370 0.108 0.018 3 0.4 S_circular_insula_ant 1571 1067 2517 2.933 0.546 0.086 0.012 6 0.7 S_circular_insula_inf 1750 1201 2709 2.856 0.377 0.086 0.013 5 1.0 S_circular_insula_sup 848 586 1628 2.796 0.683 0.118 0.023 8 0.7 S_collat_transv_ant 509 362 534 1.746 0.412 0.144 0.031 5 0.7 S_collat_transv_post 2336 1574 4413 2.655 0.550 0.100 0.017 17 1.5 S_front_inf 1414 985 1947 2.216 0.395 0.119 0.025 12 1.4 S_front_middle 2593 1815 4561 2.641 0.415 0.092 0.014 14 1.5 S_front_sup 338 257 644 2.557 0.402 0.071 0.007 1 0.1 S_interm_prim-Jensen 2959 2015 4200 2.328 0.452 0.108 0.017 20 2.1 S_intrapariet&P_trans 1167 806 1561 2.320 0.464 0.127 0.031 9 1.4 S_oc_middle&Lunatus 959 638 1253 2.212 0.409 0.096 0.016 7 0.7 S_oc_sup&transversal 548 378 926 2.473 0.417 0.119 0.020 5 0.5 S_occipital_ant 962 683 1667 2.694 0.382 0.096 0.015 5 0.5 S_oc-temp_lat 1967 1408 2911 2.310 0.371 0.097 0.013 11 1.0 S_oc-temp_med&Lingual 386 272 581 2.695 0.503 0.144 0.020 5 0.5 S_orbital_lateral 620 442 1065 2.419 0.780 0.095 0.013 4 0.3 S_orbital_med-olfact 1374 970 2595 2.677 0.599 0.138 0.036 15 2.3 S_orbital-H_Shaped 2615 1712 3696 2.373 0.573 0.115 0.022 22 2.4 S_parieto_occipital 1298 738 1033 1.942 0.773 0.122 0.019 26 0.8 S_pericallosal 3439 2306 5225 2.265 0.494 0.116 0.022 31 3.2 S_postcentral 1485 1015 2380 2.742 0.439 0.109 0.018 10 1.2 S_precentral-inf-part 1207 845 2014 2.801 0.479 0.101 0.018 6 0.9 S_precentral-sup-part 654 450 990 2.457 0.676 0.122 0.018 6 0.4 S_suborbital 789 538 1186 2.443 0.432 0.122 0.026 6 0.8 S_subparietal 1586 1171 3029 2.960 0.618 0.120 0.021 10 1.5 S_temporal_inf 5211 3644 9806 2.766 0.444 0.108 0.018 41 3.8 S_temporal_sup 440 282 533 2.343 0.554 0.102 0.011 3 0.2 S_temporal_transverse 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 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 248922 Total vertex volume 245189 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1124 764 2144 2.583 0.493 0.133 0.034 13 1.6 G&S_frontomargin 1177 811 2208 2.468 0.516 0.130 0.028 12 1.4 G&S_occipital_inf 1540 922 2434 2.323 0.522 0.117 0.029 17 1.8 G&S_paracentral 1427 989 3416 3.031 0.559 0.139 0.027 19 1.5 G&S_subcentral 1208 817 2756 2.676 0.483 0.138 0.030 18 1.5 G&S_transv_frontopol 3367 2311 7076 2.976 0.463 0.122 0.023 37 3.2 G&S_cingul-Ant 1246 901 2733 2.850 0.460 0.109 0.019 10 1.0 G&S_cingul-Mid-Ant 1477 1054 2832 2.656 0.432 0.111 0.021 11 1.3 G&S_cingul-Mid-Post 438 330 1291 2.888 0.446 0.165 0.038 9 0.7 G_cingul-Post-dorsal 298 190 691 2.833 0.617 0.142 0.035 5 0.4 G_cingul-Post-ventral 2236 1433 2685 1.732 0.467 0.141 0.035 33 3.3 G_cuneus 1244 818 3334 3.102 0.394 0.128 0.027 16 1.3 G_front_inf-Opercular 517 329 1403 2.984 0.431 0.143 0.032 10 0.6 G_front_inf-Orbital 1175 757 2897 2.874 0.403 0.136 0.027 18 1.3 G_front_inf-Triangul 3804 2456 9783 2.936 0.469 0.138 0.031 58 4.7 G_front_middle 6017 3895 15685 3.184 0.573 0.125 0.028 67 6.9 G_front_sup 774 515 1816 3.305 0.863 0.115 0.030 8 0.8 G_Ins_lg&S_cent_ins 714 458 2216 3.634 0.770 0.129 0.032 13 1.0 G_insular_short 2198 1501 5053 2.629 0.536 0.149 0.035 43 3.1 G_occipital_middle 1648 1054 2723 2.141 0.551 0.123 0.030 18 1.9 G_occipital_sup 1824 1267 4120 2.572 0.523 0.138 0.035 34 2.8 G_oc-temp_lat-fusifor 2632 1677 4065 2.042 0.584 0.143 0.037 43 4.0 G_oc-temp_med-Lingual 1102 714 2972 3.020 0.778 0.115 0.033 12 1.3 G_oc-temp_med-Parahip 2492 1740 7737 3.285 0.653 0.145 0.039 43 3.8 G_orbital 2735 1870 7004 2.911 0.443 0.149 0.035 50 3.6 G_pariet_inf-Angular 2506 1753 6534 3.041 0.399 0.139 0.030 38 3.3 G_pariet_inf-Supramar 2982 1910 6689 2.673 0.516 0.130 0.024 44 2.8 G_parietal_sup 2323 1287 3751 2.279 0.640 0.099 0.022 21 2.1 G_postcentral 3112 1729 7033 3.077 0.654 0.104 0.025 26 3.4 G_precentral 2715 1808 5293 2.456 0.477 0.126 0.023 35 2.8 G_precuneus 874 644 2139 2.435 0.661 0.140 0.034 15 1.2 G_rectus 210 151 516 3.341 0.487 0.092 0.020 2 0.1 G_subcallosal 423 239 816 2.648 0.528 0.113 0.024 4 0.3 G_temp_sup-G_T_transv 1689 1133 4946 3.266 0.486 0.136 0.030 25 2.1 G_temp_sup-Lateral 926 648 2110 3.298 0.690 0.103 0.027 5 1.1 G_temp_sup-Plan_polar 773 505 1654 2.965 0.630 0.092 0.023 6 0.6 G_temp_sup-Plan_tempo 2524 1753 7252 3.062 0.582 0.146 0.038 47 4.0 G_temporal_inf 2830 1986 8024 3.037 0.523 0.141 0.033 48 3.8 G_temporal_middle 491 355 670 2.272 0.309 0.089 0.011 2 0.2 Lat_Fis-ant-Horizont 285 207 473 2.549 0.319 0.109 0.017 1 0.3 Lat_Fis-ant-Vertical 1469 994 2047 2.536 0.569 0.104 0.017 8 1.0 Lat_Fis-post 3833 2370 4623 1.814 0.506 0.142 0.036 53 5.4 Pole_occipital 1713 1228 6160 3.552 0.733 0.151 0.038 30 2.6 Pole_temporal 2249 1567 2526 1.883 0.566 0.109 0.022 15 2.1 S_calcarine 3079 2023 3979 2.238 0.765 0.095 0.018 15 2.3 S_central 1387 959 2193 2.525 0.487 0.097 0.015 7 0.8 S_cingul-Marginalis 609 406 988 3.135 0.473 0.102 0.019 3 0.5 S_circular_insula_ant 1224 826 1870 2.891 0.474 0.085 0.011 4 0.6 S_circular_insula_inf 1437 1006 2321 2.742 0.441 0.088 0.013 5 0.8 S_circular_insula_sup 833 585 1724 2.882 0.662 0.120 0.018 7 0.7 S_collat_transv_ant 491 351 715 2.265 0.391 0.146 0.032 4 0.7 S_collat_transv_post 2151 1457 3250 2.506 0.451 0.109 0.023 15 1.8 S_front_inf 2167 1485 3518 2.455 0.379 0.116 0.021 17 1.9 S_front_middle 2020 1426 3794 2.750 0.541 0.112 0.019 14 1.6 S_front_sup 377 274 608 2.695 0.516 0.109 0.014 2 0.2 S_interm_prim-Jensen 3263 2222 5083 2.490 0.438 0.111 0.018 25 2.2 S_intrapariet&P_trans 1292 909 1820 2.286 0.448 0.122 0.022 11 1.1 S_oc_middle&Lunatus 1200 813 1311 1.880 0.389 0.107 0.018 8 0.8 S_oc_sup&transversal 663 463 981 2.549 0.413 0.110 0.019 4 0.6 S_occipital_ant 877 613 1355 2.667 0.439 0.119 0.022 7 0.6 S_oc-temp_lat 2041 1481 3104 2.452 0.423 0.096 0.013 10 1.2 S_oc-temp_med&Lingual 620 434 820 2.309 0.438 0.113 0.017 4 0.4 S_orbital_lateral 723 527 1164 2.376 0.703 0.103 0.014 5 0.4 S_orbital_med-olfact 1491 1048 2689 2.706 0.515 0.130 0.033 18 2.0 S_orbital-H_Shaped 2385 1606 3622 2.505 0.480 0.109 0.022 16 2.2 S_parieto_occipital 1436 864 1191 1.911 0.507 0.136 0.018 25 0.9 S_pericallosal 2727 1852 3933 2.339 0.469 0.097 0.016 15 1.7 S_postcentral 1817 1229 2966 2.763 0.385 0.095 0.016 9 1.1 S_precentral-inf-part 1126 791 1674 2.524 0.460 0.126 0.023 9 1.1 S_precentral-sup-part 330 234 562 2.706 0.732 0.113 0.016 2 0.3 S_suborbital 834 586 1433 2.506 0.511 0.118 0.024 7 0.8 S_subparietal 1195 839 1788 2.690 0.420 0.126 0.021 8 1.2 S_temporal_inf 5717 3971 9838 2.584 0.415 0.094 0.015 33 3.4 S_temporal_sup 361 242 566 2.865 0.498 0.105 0.011 2 0.2 S_temporal_transverse PIDs (2225 2228) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Wed Jan 18 23:38:48 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Wed Jan 18 23:38:48 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 2413 of (2413 2416) to complete... Waiting for PID 2416 of (2413 2416) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1631 labels changed using aseg relabeling using gibbs priors... 000: 1908 changed, 133349 examined... 001: 468 changed, 8642 examined... 002: 140 changed, 2637 examined... 003: 64 changed, 797 examined... 004: 38 changed, 362 examined... 005: 18 changed, 218 examined... 006: 9 changed, 101 examined... 007: 6 changed, 47 examined... 008: 7 changed, 35 examined... 009: 7 changed, 37 examined... 010: 5 changed, 38 examined... 011: 4 changed, 28 examined... 012: 2 changed, 22 examined... 013: 4 changed, 16 examined... 014: 1 changed, 20 examined... 015: 2 changed, 5 examined... 016: 1 changed, 9 examined... 017: 1 changed, 7 examined... 018: 0 changed, 6 examined... 278 labels changed using aseg 000: 57 total segments, 24 labels (225 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... 673 vertices marked for relabeling... 673 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot 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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1730 labels changed using aseg relabeling using gibbs priors... 000: 1839 changed, 133018 examined... 001: 435 changed, 8687 examined... 002: 122 changed, 2495 examined... 003: 54 changed, 691 examined... 004: 34 changed, 312 examined... 005: 18 changed, 195 examined... 006: 16 changed, 106 examined... 007: 10 changed, 78 examined... 008: 10 changed, 53 examined... 009: 7 changed, 45 examined... 010: 5 changed, 35 examined... 011: 4 changed, 23 examined... 012: 3 changed, 21 examined... 013: 3 changed, 19 examined... 014: 1 changed, 18 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 1 changed, 7 examined... 018: 1 changed, 7 examined... 019: 1 changed, 7 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 0 changed, 9 examined... 288 labels changed using aseg 000: 46 total segments, 13 labels (49 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 631 vertices marked for relabeling... 631 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 12 seconds. PIDs (2413 2416) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Jan 18 23:39:00 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab bert lh white #----------------------------------------- #@# Parcellation Stats 3 rh Wed Jan 18 23:39:00 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab bert rh white Waiting for PID 2510 of (2510 2513) to complete... Waiting for PID 2513 of (2510 2513) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab bert lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 250241 Total vertex volume 246969 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1655 1137 3218 2.817 0.508 0.116 0.014 18 0.9 caudalanteriorcingulate 2973 1973 6286 2.840 0.533 0.114 0.021 28 2.5 caudalmiddlefrontal 3606 2280 4631 1.952 0.542 0.136 0.031 48 4.8 cuneus 456 340 1575 3.352 0.618 0.115 0.021 4 0.4 entorhinal 3855 2678 7504 2.642 0.577 0.129 0.025 46 3.7 fusiform 5241 3639 10660 2.670 0.494 0.127 0.027 71 5.5 inferiorparietal 5009 3524 12893 3.034 0.619 0.139 0.033 73 6.8 inferiortemporal 1452 920 2238 2.149 0.755 0.120 0.025 21 1.3 isthmuscingulate 8014 5091 12906 2.325 0.570 0.137 0.033 103 10.7 lateraloccipital 3912 2733 9188 2.880 0.681 0.145 0.038 60 6.6 lateralorbitofrontal 4603 3059 5952 1.861 0.497 0.129 0.029 59 5.7 lingual 2461 1739 5226 2.468 0.787 0.127 0.040 50 4.5 medialorbitofrontal 6089 4161 14556 3.051 0.594 0.126 0.026 72 6.4 middletemporal 970 642 1747 2.497 0.589 0.071 0.012 4 0.4 parahippocampal 2418 1574 4447 2.594 0.630 0.100 0.023 15 2.3 paracentral 2174 1505 5019 2.938 0.529 0.117 0.019 20 1.7 parsopercularis 1074 725 2340 2.839 0.490 0.109 0.018 10 0.8 parsorbitalis 2819 1864 5700 2.797 0.500 0.114 0.021 30 2.3 parstriangularis 1889 1262 1789 1.589 0.415 0.126 0.029 19 2.0 pericalcarine 6638 4246 10549 2.268 0.676 0.107 0.022 55 5.8 postcentral 1880 1292 3404 2.431 0.564 0.125 0.022 24 1.7 posteriorcingulate 7161 4475 14420 2.993 0.648 0.102 0.021 50 6.4 precentral 5254 3523 9117 2.460 0.534 0.122 0.024 57 5.0 precuneus 1467 971 2980 2.976 0.697 0.123 0.024 18 1.3 rostralanteriorcingulate 6071 4067 11632 2.597 0.559 0.126 0.027 75 6.4 rostralmiddlefrontal 11478 7827 26401 2.938 0.603 0.124 0.027 125 12.6 superiorfrontal 6254 4137 11369 2.445 0.526 0.122 0.024 72 5.8 superiorparietal 7462 5142 17907 3.028 0.606 0.116 0.024 75 6.9 superiortemporal 6328 4302 13205 2.779 0.556 0.124 0.023 71 5.8 supramarginal 759 476 1217 2.434 0.522 0.133 0.022 9 0.7 transversetemporal 3104 2084 6892 3.246 0.615 0.095 0.017 23 2.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab bert rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 248922 Total vertex volume 245189 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1161 803 2410 2.562 0.648 0.137 0.020 17 1.0 caudalanteriorcingulate 2658 1785 5422 2.882 0.486 0.110 0.020 20 2.1 caudalmiddlefrontal 2954 1897 3827 1.938 0.525 0.133 0.031 39 3.9 cuneus 426 309 1620 3.507 0.555 0.129 0.032 4 0.6 entorhinal 3705 2604 7085 2.582 0.551 0.128 0.029 49 4.4 fusiform 6708 4667 14267 2.738 0.468 0.126 0.025 81 6.7 inferiorparietal 4715 3326 12075 3.001 0.629 0.136 0.031 68 6.1 inferiortemporal 1211 790 1981 2.286 0.712 0.123 0.028 17 1.2 isthmuscingulate 8566 5624 12756 2.125 0.559 0.135 0.031 109 10.7 lateraloccipital 4356 3057 10028 2.966 0.705 0.139 0.038 64 6.6 lateralorbitofrontal 4298 2867 6181 2.028 0.551 0.132 0.032 55 5.8 lingual 2257 1628 4908 2.648 0.717 0.123 0.025 28 2.1 medialorbitofrontal 5742 4015 13693 2.910 0.572 0.127 0.027 75 6.3 middletemporal 1064 698 1988 2.612 0.619 0.084 0.017 8 0.5 parahippocampal 2435 1580 4142 2.512 0.514 0.110 0.023 20 2.3 paracentral 2284 1557 4822 2.933 0.466 0.120 0.024 22 2.1 parsopercularis 1253 835 3139 3.037 0.499 0.129 0.025 16 1.4 parsorbitalis 2537 1695 4914 2.641 0.452 0.122 0.024 28 2.4 parstriangularis 1940 1277 1974 1.759 0.556 0.112 0.024 13 1.8 pericalcarine 6901 4305 10853 2.282 0.689 0.102 0.020 58 5.7 postcentral 1761 1262 3515 2.559 0.570 0.138 0.025 24 1.9 posteriorcingulate 7443 4632 14803 2.883 0.636 0.104 0.022 54 7.1 precentral 5766 3925 10157 2.494 0.491 0.118 0.022 55 5.4 precuneus 1206 820 2683 2.939 0.543 0.134 0.022 17 1.1 rostralanteriorcingulate 5961 3968 11863 2.600 0.502 0.128 0.028 68 6.6 rostralmiddlefrontal 12367 8268 27412 2.956 0.573 0.120 0.025 126 12.5 superiorfrontal 6781 4459 12340 2.440 0.510 0.117 0.021 73 5.6 superiorparietal 6604 4492 15473 3.044 0.617 0.111 0.024 62 6.1 superiortemporal 5307 3663 10900 2.770 0.522 0.120 0.022 55 5.0 supramarginal 554 330 848 2.387 0.477 0.116 0.022 5 0.4 transversetemporal 3293 2217 7111 3.220 0.673 0.105 0.020 28 2.6 insula PIDs (2510 2513) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Wed Jan 18 23:39:29 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts pctsurfcon --s bert --lh-only #----------------------------------------- #@# WM/GM Contrast rh Wed Jan 18 23:39:29 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts pctsurfcon --s bert --rh-only Waiting for PID 2690 of (2690 2693) to complete... Waiting for PID 2693 of (2690 2693) to complete... pctsurfcon --s bert --lh-only Log file is /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts/pctsurfcon.log Wed Jan 18 23:39:29 EST 2017 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects cd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts /usr/local/freesurfer/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux terrier 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/freesurfer mri_vol2surf --mov /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2690/lh.wm.mgh --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label Reading surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 = 74221 Masking with /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label Writing to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2690/lh.wm.mgh Dim: 133349 1 1 mri_vol2surf --mov /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2690/lh.gm.mgh --projfrac 0.3 --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label Reading surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 = 88254 Masking with /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.cortex.label Writing to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2690/lh.gm.mgh Dim: 133349 1 1 mri_concat /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2690/lh.wm.mgh /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2690/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.w-g.pct.mgh --annot bert lh aparc --sum /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.w-g.pct.mgh --annot bert lh aparc --sum /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/stats/lh.w-g.pct.stats --snr sysname Linux hostname terrier machine x86_64 user zkaufman UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.w-g.pct.mgh Vertex Area is 0.669022 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 pctsurfcon --s bert --rh-only Log file is /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts/pctsurfcon.log Wed Jan 18 23:39:29 EST 2017 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects cd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/scripts /usr/local/freesurfer/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux terrier 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/freesurfer mri_vol2surf --mov /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2693/rh.wm.mgh --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label Reading surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 = 74119 Masking with /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label Writing to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2693/rh.wm.mgh Dim: 133018 1 1 mri_vol2surf --mov /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2693/rh.gm.mgh --projfrac 0.3 --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label Reading surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 = 88426 Masking with /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.cortex.label Writing to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2693/rh.gm.mgh Dim: 133018 1 1 mri_concat /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2693/rh.wm.mgh /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/tmp.pctsurfcon.2693/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.w-g.pct.mgh --annot bert rh aparc --sum /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.w-g.pct.mgh --annot bert rh aparc --sum /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/stats/rh.w-g.pct.stats --snr sysname Linux hostname terrier machine x86_64 user zkaufman UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.w-g.pct.mgh Vertex Area is 0.671589 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 PIDs (2690 2693) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Wed Jan 18 23:39:35 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2860 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3387 voxels changed to hypointensity... 6218 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed Jan 18 23:39:53 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert mri_aparc2aseg --s bert --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Wed Jan 18 23:39:53 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert mri_aparc2aseg --s bert --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed Jan 18 23:39:53 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert mri_aparc2aseg --s bert --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Waiting for PID 2965 of (2965 2968 2971) to complete... Waiting for PID 2968 of (2965 2968 2971) to complete... Waiting for PID 2971 of (2965 2968 2971) to complete... mri_aparc2aseg --s bert --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects subject bert outvol /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.67 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 92 rescaling Left_Cerebellum_Cortex from 60 --> 78 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 43 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 62 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 78 rescaling Right_Lateral_Ventricle from 13 --> 26 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 81 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 79 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 52 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 489562 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 102 changed. pass 2: 4 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aparc+aseg.mgz mri_aparc2aseg --s bert --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects subject bert outvol /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.67 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 92 rescaling Left_Cerebellum_Cortex from 60 --> 78 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 43 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 62 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 78 rescaling Right_Lateral_Ventricle from 13 --> 26 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 81 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 79 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 52 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 489595 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 102 changed. pass 2: 4 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s bert --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects subject bert outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.67 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 25 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 92 rescaling Left_Cerebellum_Cortex from 60 --> 78 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 43 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 62 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 78 rescaling Right_Lateral_Ventricle from 13 --> 26 rescaling Right_Inf_Lat_Vent from 25 --> 30 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 81 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 79 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 52 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 489595 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 102 changed. pass 2: 4 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (2965 2968 2971) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Wed Jan 18 23:43:50 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Wed Jan 18 23:43:50 EST 2017 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects cd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri /usr/local/freesurfer/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux terrier 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 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 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri cmdline mri_binarize.bin --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 Linux hostname terrier 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 18 23:43:50 EST 2017 Ended at Wed Jan 18 23:43:55 EST 2017 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed Jan 18 23:43:55 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert 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/freesurfer/ASegStatsLUT.txt --subject bert $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 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/freesurfer/ASegStatsLUT.txt --subject bert sysname Linux hostname terrier machine x86_64 user zkaufman UseRobust 0 atlas_icv (eTIV) = 1602572 mm^3 (det: 1.215612 ) Computing euler number orig.nofix lheno = -66, rheno = -58 orig.nofix lhholes = 34, rhholes = 30 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 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 18 23:44:56 EST 2017 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert mri_aparc2aseg --s bert --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects subject bert outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/ribbon.mgz Loading filled from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8847 vertices from left hemi Ripped 8839 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 = 977451 Used brute-force search on 59 voxels Fixing Parahip LH WM Found 17 clusters 0 k 5.000000 1 k 1.000000 2 k 3.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 3.000000 7 k 3.000000 8 k 1.000000 9 k 1.000000 10 k 3.000000 11 k 1.000000 12 k 1.000000 13 k 3.000000 14 k 1.000000 15 k 1.000000 16 k 1576.000000 Fixing Parahip RH WM Found 6 clusters 0 k 1.000000 1 k 1.000000 2 k 1803.000000 3 k 1.000000 4 k 1.000000 5 k 3.000000 Writing output aseg to mri/wmparc.mgz 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 --surf-wm-vol --ctab /usr/local/freesurfer/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 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 --surf-wm-vol --ctab /usr/local/freesurfer/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname terrier 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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Jan 18 23:50:33 EST 2017 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject bert --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject bert --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject bert --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject bert --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject bert --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 6182 of (6182 6187 6194 6200 6206) to complete... Waiting for PID 6187 of (6182 6187 6194 6200 6206) to complete... Waiting for PID 6194 of (6182 6187 6194 6200 6206) to complete... Waiting for PID 6200 of (6182 6187 6194 6200 6206) to complete... Waiting for PID 6206 of (6182 6187 6194 6200 6206) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject bert --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4378 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject bert --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 448 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8357 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject bert --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4178 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject bert --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 257 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6240 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject bert --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6213 mri_label2label: Done PIDs (6182 6187 6194 6200 6206) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject bert --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject bert --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject bert --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject bert --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 6298 of (6298 6304 6310 6316) to complete... Waiting for PID 6304 of (6298 6304 6310 6316) to complete... Waiting for PID 6310 of (6298 6304 6310 6316) to complete... Waiting for PID 6316 of (6298 6304 6310 6316) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject bert --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4294 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject bert --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 694 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject bert --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4373 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject bert --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 856 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4278 mri_label2label: Done PIDs (6298 6304 6310 6316) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject bert --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject bert --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject bert --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject bert --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject bert --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 6406 of (6406 6412 6418 6424 6430) to complete... Waiting for PID 6412 of (6406 6412 6418 6424 6430) to complete... Waiting for PID 6418 of (6406 6412 6418 6424 6430) to complete... Waiting for PID 6424 of (6406 6412 6418 6424 6430) to complete... Waiting for PID 6430 of (6406 6412 6418 6424 6430) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject bert --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 1382 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6023 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject bert --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 3035 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11149 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject bert --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 488 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2506 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject bert --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1339 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject bert --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1235 mri_label2label: Done PIDs (6406 6412 6418 6424 6430) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 6527 of (6527 6533 6539 6545 6551) to complete... Waiting for PID 6533 of (6527 6533 6539 6545 6551) to complete... Waiting for PID 6539 of (6527 6533 6539 6545 6551) to complete... Waiting for PID 6545 of (6527 6533 6539 6545 6551) to complete... Waiting for PID 6551 of (6527 6533 6539 6545 6551) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1078 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2168 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2057 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2522 mri_label2label: Done PIDs (6527 6533 6539 6545 6551) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 6632 of (6632 6638 6644 6650) to complete... Waiting for PID 6638 of (6632 6638 6644 6650) to complete... Waiting for PID 6644 of (6632 6638 6644 6650) to complete... Waiting for PID 6650 of (6632 6638 6644 6650) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1623 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7342 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1990 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 354 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1505 mri_label2label: Done PIDs (6632 6638 6644 6650) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject bert --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject bert --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject bert --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject bert --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject bert --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 6731 of (6731 6737 6743 6749 6755) to complete... Waiting for PID 6737 of (6731 6737 6743 6749 6755) to complete... Waiting for PID 6743 of (6731 6737 6743 6749 6755) to complete... Waiting for PID 6749 of (6731 6737 6743 6749 6755) to complete... Waiting for PID 6755 of (6731 6737 6743 6749 6755) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject bert --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 878 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject bert --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 1456 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4790 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject bert --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 662 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject bert --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 492 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject bert --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133349 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 454 mri_label2label: Done PIDs (6731 6737 6743 6749 6755) completed and logs appended. mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/freesurfer/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 Reading ctab /usr/local/freesurfer/freesurfer/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/centos6_x86_64/freesurfer/subjects/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/freesurfer/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 Linux hostname terrier machine x86_64 user zkaufman subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects ColorTable /usr/local/freesurfer/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 92742 unhit vertices Writing annot to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.BA_exvivo.annot mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/freesurfer/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 Reading ctab /usr/local/freesurfer/freesurfer/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/centos6_x86_64/freesurfer/subjects/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/freesurfer/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 Linux hostname terrier machine x86_64 user zkaufman subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects ColorTable /usr/local/freesurfer/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 109647 unhit vertices Writing annot to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab bert lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 250241 Total vertex volume 246969 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/freesurfer/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 1074 602 2017 2.480 0.552 0.119 0.030 12 1.2 BA1_exvivo 3863 2574 6003 2.286 0.507 0.110 0.021 31 3.3 BA2_exvivo 1047 711 1074 1.959 0.374 0.125 0.023 8 1.0 BA3a_exvivo 2234 1448 3203 1.990 0.643 0.096 0.021 16 2.1 BA3b_exvivo 1746 1014 3350 2.836 0.728 0.096 0.030 14 2.2 BA4a_exvivo 1355 861 2398 2.889 0.594 0.086 0.018 5 1.1 BA4p_exvivo 8319 5413 19734 3.115 0.613 0.110 0.024 70 8.0 BA6_exvivo 2011 1418 4711 2.914 0.544 0.127 0.023 21 2.0 BA44_exvivo 3436 2301 7258 2.805 0.525 0.126 0.025 41 3.4 BA45_exvivo 3527 2259 3615 1.623 0.456 0.128 0.031 39 4.4 V1_exvivo 8733 5553 11640 1.986 0.539 0.138 0.035 116 12.5 V2_exvivo 2142 1443 3716 2.603 0.425 0.133 0.025 26 2.2 MT_exvivo 552 382 1434 2.955 0.781 0.107 0.025 4 0.6 perirhinal_exvivo 568 410 1092 2.756 0.596 0.091 0.015 3 0.3 entorhinal_exvivo 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 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 250241 Total vertex volume 246969 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/freesurfer/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 662 339 1183 2.477 0.582 0.124 0.041 9 1.1 BA1_exvivo 1355 903 2173 2.246 0.492 0.092 0.016 7 0.9 BA2_exvivo 868 593 854 1.927 0.336 0.130 0.025 7 0.9 BA3a_exvivo 1295 867 1532 1.686 0.483 0.071 0.011 4 0.6 BA3b_exvivo 1670 989 3169 2.852 0.749 0.087 0.025 9 1.7 BA4a_exvivo 1094 704 1823 2.747 0.598 0.089 0.020 5 1.0 BA4p_exvivo 4643 2845 10695 3.134 0.607 0.102 0.025 37 4.9 BA6_exvivo 1335 952 3066 2.871 0.531 0.131 0.023 16 1.3 BA44_exvivo 1398 934 3187 2.949 0.508 0.128 0.024 17 1.2 BA45_exvivo 3746 2403 3859 1.608 0.446 0.123 0.030 38 4.6 V1_exvivo 4458 2739 5357 1.902 0.518 0.141 0.038 65 6.9 V2_exvivo 609 402 1326 2.771 0.484 0.137 0.027 9 0.6 MT_exvivo 283 190 789 2.952 0.803 0.093 0.019 1 0.3 perirhinal_exvivo 286 212 661 2.982 0.465 0.071 0.009 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Wed Jan 18 23:52:14 EST 2017 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject bert --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject bert --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject bert --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject bert --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject bert --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 7083 of (7083 7088 7095 7101 7107) to complete... Waiting for PID 7088 of (7083 7088 7095 7101 7107) to complete... Waiting for PID 7095 of (7083 7088 7095 7101 7107) to complete... Waiting for PID 7101 of (7083 7088 7095 7101 7107) to complete... Waiting for PID 7107 of (7083 7088 7095 7101 7107) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject bert --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4226 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject bert --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 377 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7064 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject bert --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4122 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject bert --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 253 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4775 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject bert --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 406 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6153 mri_label2label: Done PIDs (7083 7088 7095 7101 7107) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject bert --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject bert --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject bert --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject bert --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 7191 of (7191 7197 7203 7209) to complete... Waiting for PID 7197 of (7191 7197 7203 7209) to complete... Waiting for PID 7203 of (7191 7197 7203 7209) to complete... Waiting for PID 7209 of (7191 7197 7203 7209) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject bert --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 257 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4730 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject bert --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 700 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12956 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject bert --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 813 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7725 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject bert --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 1142 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6497 mri_label2label: Done PIDs (7191 7197 7203 7209) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject bert --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject bert --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject bert --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject bert --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject bert --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 7300 of (7300 7306 7312 7318 7324) to complete... Waiting for PID 7306 of (7300 7306 7312 7318 7324) to complete... Waiting for PID 7312 of (7300 7306 7312 7318 7324) to complete... Waiting for PID 7318 of (7300 7306 7312 7318 7324) to complete... Waiting for PID 7324 of (7300 7306 7312 7318 7324) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject bert --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 1440 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6167 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject bert --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 3012 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11028 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject bert --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 322 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2254 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject bert --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject bert --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 778 mri_label2label: Done PIDs (7300 7306 7312 7318 7324) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 7417 of (7417 7423 7429 7435 7441) to complete... Waiting for PID 7423 of (7417 7423 7429 7435 7441) to complete... Waiting for PID 7429 of (7417 7423 7429 7435 7441) to complete... Waiting for PID 7435 of (7417 7423 7429 7435 7441) to complete... Waiting for PID 7441 of (7417 7423 7429 7435 7441) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 979 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2798 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1754 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2281 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1504 mri_label2label: Done PIDs (7417 7423 7429 7435 7441) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 7526 of (7526 7532 7538 7544) to complete... Waiting for PID 7532 of (7526 7532 7538 7544) to complete... Waiting for PID 7538 of (7526 7532 7538 7544) to complete... Waiting for PID 7544 of (7526 7532 7538 7544) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7309 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1109 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1401 mri_label2label: Done PIDs (7526 7532 7538 7544) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject bert --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject bert --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject bert --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject bert --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject bert --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 7627 of (7627 7633 7639 7645 7651) to complete... Waiting for PID 7633 of (7627 7633 7639 7645 7651) to complete... Waiting for PID 7639 of (7627 7633 7639 7645 7651) to complete... Waiting for PID 7645 of (7627 7633 7639 7645 7651) to complete... Waiting for PID 7651 of (7627 7633 7639 7645 7651) to complete... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject bert --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 817 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4049 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject bert --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 1370 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4807 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject bert --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject bert --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 721 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject bert --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 133018 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 295 mri_label2label: Done PIDs (7627 7633 7639 7645 7651) completed and logs appended. mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/freesurfer/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 Reading ctab /usr/local/freesurfer/freesurfer/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/centos6_x86_64/freesurfer/subjects/bert/label cmdline mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/freesurfer/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 Linux hostname terrier machine x86_64 user zkaufman subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects ColorTable /usr/local/freesurfer/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 92485 unhit vertices Writing annot to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.BA_exvivo.annot mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/freesurfer/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 Reading ctab /usr/local/freesurfer/freesurfer/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/centos6_x86_64/freesurfer/subjects/bert/label cmdline mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/freesurfer/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 Linux hostname terrier machine x86_64 user zkaufman subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects ColorTable /usr/local/freesurfer/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/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 110601 unhit vertices Writing annot to /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab bert rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 248922 Total vertex volume 245189 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/freesurfer/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 998 505 1755 2.424 0.558 0.112 0.027 13 1.1 BA1_exvivo 3345 2161 5286 2.390 0.524 0.099 0.018 21 2.3 BA2_exvivo 1129 754 1094 1.927 0.424 0.123 0.027 9 1.2 BA3a_exvivo 1968 1236 2498 1.807 0.598 0.094 0.018 13 1.5 BA3b_exvivo 1724 1018 3178 2.761 0.608 0.106 0.026 13 2.1 BA4a_exvivo 1250 824 2223 2.836 0.624 0.094 0.021 6 1.1 BA4p_exvivo 7074 4457 15640 2.996 0.642 0.110 0.023 57 6.7 BA6_exvivo 3579 2418 7512 2.890 0.470 0.109 0.020 28 2.8 BA44_exvivo 4694 3135 9851 2.740 0.517 0.127 0.026 55 5.1 BA45_exvivo 3704 2362 4176 1.737 0.526 0.117 0.028 35 4.3 V1_exvivo 8478 5533 11331 1.957 0.526 0.143 0.035 118 12.0 V2_exvivo 1788 1248 3282 2.644 0.415 0.119 0.023 16 1.9 MT_exvivo 493 347 1581 3.251 0.635 0.109 0.024 4 0.5 perirhinal_exvivo 309 219 675 2.958 0.598 0.101 0.015 2 0.2 entorhinal_exvivo 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 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/centos6_x86_64/freesurfer/subjects/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 248922 Total vertex volume 245189 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/freesurfer/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: 246946.643 246418.000 diff= 528.6 pctdiff= 0.214 rhCtxGM: 245159.188 244943.000 diff= 216.2 pctdiff= 0.088 lhCtxWM: 244933.612 245585.500 diff= -651.9 pctdiff=-0.266 rhCtxWM: 244547.797 245138.500 diff= -590.7 pctdiff=-0.242 SubCortGMVol 60974.000 SupraTentVol 1059323.239 (1057941.000) diff=1382.239 pctdiff=0.130 SupraTentVolNotVent 1044470.239 (1043088.000) diff=1382.239 pctdiff=0.132 BrainSegVol 1219701.000 (1217125.000) diff=2576.000 pctdiff=0.211 BrainSegVolNotVent 1201279.000 (1200543.239) diff=735.761 pctdiff=0.061 BrainSegVolNotVent 1201279.000 CerebellumVol 157953.000 VentChorVol 14853.000 3rd4th5thCSF 3569.000 CSFVol 993.000, OptChiasmVol 238.000 MaskVol 1801725.000 721 347 1123 2.296 0.563 0.105 0.025 9 0.8 BA1_exvivo 1815 1138 3053 2.451 0.515 0.085 0.014 9 0.9 BA2_exvivo 1007 664 926 1.960 0.433 0.125 0.027 7 1.1 BA3a_exvivo 1536 989 1672 1.662 0.471 0.079 0.012 6 0.7 BA3b_exvivo 1031 597 1557 2.490 0.592 0.113 0.034 8 1.7 BA4a_exvivo 1004 687 1861 2.907 0.682 0.095 0.021 5 0.9 BA4p_exvivo 4574 2865 9658 2.926 0.662 0.108 0.022 34 4.1 BA6_exvivo 875 597 2190 3.055 0.380 0.123 0.024 10 0.8 BA44_exvivo 1240 824 2947 2.854 0.428 0.127 0.023 16 1.1 BA45_exvivo 3507 2255 3883 1.726 0.520 0.115 0.027 30 3.8 V1_exvivo 4375 2780 5227 1.787 0.498 0.147 0.040 68 7.1 V2_exvivo 232 159 515 2.586 0.320 0.135 0.030 3 0.3 MT_exvivo 308 207 1003 3.293 0.604 0.117 0.025 3 0.4 perirhinal_exvivo 192 146 525 3.224 0.463 0.088 0.014 1 0.1 entorhinal_exvivo Started at Wed Jan 18 18:13:10 EST 2017 Ended at Wed Jan 18 23:53:52 EST 2017 #@#%# recon-all-run-time-hours 5.678 recon-all -s bert finished without error at Wed Jan 18 23:53:52 EST 2017 New invocation of recon-all Thu Sep 28 10:04:44 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2918624 4447948 596364 4806056 8286512 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:04:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 10:04:44 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_10645_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 10:05:09 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 10:07:35 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2905356 4429672 614568 4837600 8281600 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:07:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 10:07:35 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_11027_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 10:07:59 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 10:30:28 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2961932 4364696 615156 4846000 8224452 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:30:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 10:30:29 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_11991_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 10:30:52 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 10:36:37 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2977636 4294944 641764 4900048 8182168 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-17:36:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 10:36:37 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_12403_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 10:37:00 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 11:05:58 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2934780 4295388 587576 4942460 8279104 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:58-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:58-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:05:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 11:05:59 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_14079_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 11:06:22 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 11:12:11 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2937380 4286276 588872 4948972 8275376 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/28-18:12:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 11:12:11 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_15192_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 11:12:35 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 11:31:15 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20170915- Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2377256 758776 571160 9036596 8853476 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_normalize.c,v 1.92 2017/01/27 22:31:34 ah221 Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_label2label.c,v 1.50 2016/12/10 22:57:43 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:16-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:17-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:31:18-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 11:31:18 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... -------------------------------------------------------------------------- ERROR: FreeSurfer license file /usr/local/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. -------------------------------------------------------------------------- conforming output volume setting resolution for intermediate calculations to 1.0000 ERROR: mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 11:31:18 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Sep 28 11:32:42 PDT 2017 /home/michael/Documents/Subjects/bert /usr/local/freesurfer/bin/recon-all -s bert -localGI subjid bert setenv SUBJECTS_DIR /home/michael/Documents/Subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20170915- Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 46503 maxlocks unlimited maxsignal 46503 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12172628 2410904 620140 575892 9141584 8815148 Swap: 12451836 0 12451836 ######################################## program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_normalize.c,v 1.92 2017/01/27 22:31:34 ah221 Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_label2label.c,v 1.50 2016/12/10 22:57:43 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/28-18:32:42-GMT BuildTimeStamp: Sep 15 2017 00:02:29 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: michael Machine: michael-M11AD Platform: Linux PlatformVersion: 4.10.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/michael/Documents/Subjects/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Sep 28 11:32:42 PDT 2017 mris_compute_lgi --i lh.pial ================= rm -Rf /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 66748 voxel in cpt #1: X=2 [v=66748,e=200238,f=133492] located at (-25.354359, -13.925411, 15.344460) For the whole surface: X=2 [v=66748,e=200238,f=133492] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 66748 - 200238 + 133492 = 2 --> 0 holes F =2V-4: 133492 = 133496-4 (0) 2E=3F: 400476 = 400476 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/home/michael/Documents/Subjects/bert/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_16713_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic Student License -- for use by students to meet course requirements and perform academic research at degree granting institutions only. >> FREESURFER_READ_SURF [v 1.2 ] {Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); } >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Thu Sep 28 11:33:12 PDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting