Tue May 25 21:12:54 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-05 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-05 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux blg4313.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638428 111601596 72261296 2007648 12775536 79944380 Swap: 0 0 0 ######################################## 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: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-21:12:54-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Tessellate lh Tue May 25 21:12:55 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 5 found - 5 modified | TOTAL: 6 pass 2 (yz+): 0 found - 5 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 modified | TOTAL: 12 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 16 (out of 493601: 0.003241) 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 50: 3624 vertices, 3864 faces slice 60: 13548 vertices, 14008 faces slice 70: 28521 vertices, 29028 faces slice 80: 43694 vertices, 44210 faces slice 90: 58110 vertices, 58579 faces slice 100: 72624 vertices, 73100 faces slice 110: 86834 vertices, 87334 faces slice 120: 101833 vertices, 102403 faces slice 130: 116861 vertices, 117395 faces slice 140: 130674 vertices, 131222 faces slice 150: 144581 vertices, 145153 faces slice 160: 158170 vertices, 158763 faces slice 170: 171330 vertices, 171912 faces slice 180: 182435 vertices, 182947 faces slice 190: 192329 vertices, 192816 faces slice 200: 201315 vertices, 201780 faces slice 210: 208912 vertices, 209355 faces slice 220: 215880 vertices, 216257 faces slice 230: 221076 vertices, 221428 faces slice 240: 224169 vertices, 224400 faces slice 250: 224390 vertices, 224576 faces slice 260: 224390 vertices, 224576 faces slice 270: 224390 vertices, 224576 faces slice 280: 224390 vertices, 224576 faces slice 290: 224390 vertices, 224576 faces slice 300: 224390 vertices, 224576 faces slice 310: 224390 vertices, 224576 faces slice 320: 224390 vertices, 224576 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -0.80000 0.00000 0.00000 127.99999; 0.00000 0.00000 0.80000 -127.99999; 0.00000 -0.80000 0.00000 127.99999; 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... 224390 voxel in cpt #1: X=-186 [v=224390,e=673728,f=449152] located at (-29.555977, -24.653690, 19.072826) For the whole surface: X=-186 [v=224390,e=673728,f=449152] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue May 25 21:13:03 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts 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... #-------------------------------------------- #@# Inflation1 lh Tue May 25 21:13:12 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_inflate -no-save-sulc -n 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix niterations = 50 Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.6 mm, total surface area = 78814 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 2.3 minutes step 000: RMS=0.146 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.038 (target=0.015) step 065: RMS=0.038 (target=0.015) step 070: RMS=0.037 (target=0.015) step 075: RMS=0.037 (target=0.015) step 080: RMS=0.037 (target=0.015) step 085: RMS=0.037 (target=0.015) step 090: RMS=0.036 (target=0.015) step 095: RMS=0.036 (target=0.015) step 100: RMS=0.036 (target=0.015) step 105: RMS=0.036 (target=0.015) step 110: RMS=0.036 (target=0.015) step 115: RMS=0.036 (target=0.015) step 120: RMS=0.035 (target=0.015) step 125: RMS=0.035 (target=0.015) step 130: RMS=0.035 (target=0.015) step 135: RMS=0.035 (target=0.015) step 140: RMS=0.035 (target=0.015) step 145: RMS=0.035 (target=0.015) step 150: RMS=0.035 (target=0.015) step 155: RMS=0.035 (target=0.015) step 160: RMS=0.035 (target=0.015) step 165: RMS=0.035 (target=0.015) step 170: RMS=0.035 (target=0.015) step 175: RMS=0.035 (target=0.015) step 180: RMS=0.035 (target=0.015) step 185: RMS=0.035 (target=0.015) step 190: RMS=0.035 (target=0.015) step 195: RMS=0.035 (target=0.015) step 200: RMS=0.035 (target=0.015) step 205: RMS=0.035 (target=0.015) step 210: RMS=0.035 (target=0.015) step 215: RMS=0.035 (target=0.015) step 220: RMS=0.035 (target=0.015) step 225: RMS=0.035 (target=0.015) step 230: RMS=0.035 (target=0.015) step 235: RMS=0.035 (target=0.015) step 240: RMS=0.035 (target=0.015) step 245: RMS=0.035 (target=0.015) step 250: RMS=0.035 (target=0.015) step 255: RMS=0.036 (target=0.015) step 260: RMS=0.037 (target=0.015) step 265: RMS=0.037 (target=0.015) step 270: RMS=0.037 (target=0.015) step 275: RMS=0.037 (target=0.015) step 280: RMS=0.037 (target=0.015) step 285: RMS=0.037 (target=0.015) step 290: RMS=0.036 (target=0.015) step 295: RMS=0.036 (target=0.015) step 300: RMS=0.036 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 671.174818 mris_inflate stimesec 11.221308 mris_inflate ru_maxrss 358756 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 3612705 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 15792 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 145327 mris_inflate ru_nivcsw 4314 #-------------------------------------------- #@# QSphere lh Tue May 25 21:15:29 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 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 0.76 +- 0.44 (0.00-->6.87) (max @ vno 160481 --> 160497) face area 0.02 +- 0.02 (-0.11-->0.39) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.310... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.624, avgs=0 005/300: dt: 0.9000, rms radial error=174.363, avgs=0 010/300: dt: 0.9000, rms radial error=173.804, avgs=0 015/300: dt: 0.9000, rms radial error=173.068, avgs=0 020/300: dt: 0.9000, rms radial error=172.229, avgs=0 025/300: dt: 0.9000, rms radial error=171.333, avgs=0 030/300: dt: 0.9000, rms radial error=170.409, avgs=0 035/300: dt: 0.9000, rms radial error=169.475, avgs=0 040/300: dt: 0.9000, rms radial error=168.533, avgs=0 045/300: dt: 0.9000, rms radial error=167.590, avgs=0 050/300: dt: 0.9000, rms radial error=166.647, avgs=0 055/300: dt: 0.9000, rms radial error=165.707, avgs=0 060/300: dt: 0.9000, rms radial error=164.771, avgs=0 065/300: dt: 0.9000, rms radial error=163.840, avgs=0 070/300: dt: 0.9000, rms radial error=162.913, avgs=0 075/300: dt: 0.9000, rms radial error=161.991, avgs=0 080/300: dt: 0.9000, rms radial error=161.074, avgs=0 085/300: dt: 0.9000, rms radial error=160.162, avgs=0 090/300: dt: 0.9000, rms radial error=159.255, avgs=0 095/300: dt: 0.9000, rms radial error=158.354, avgs=0 100/300: dt: 0.9000, rms radial error=157.457, avgs=0 105/300: dt: 0.9000, rms radial error=156.566, avgs=0 110/300: dt: 0.9000, rms radial error=155.680, avgs=0 115/300: dt: 0.9000, rms radial error=154.799, avgs=0 120/300: dt: 0.9000, rms radial error=153.924, avgs=0 125/300: dt: 0.9000, rms radial error=153.053, avgs=0 130/300: dt: 0.9000, rms radial error=152.186, avgs=0 135/300: dt: 0.9000, rms radial error=151.325, avgs=0 140/300: dt: 0.9000, rms radial error=150.469, avgs=0 145/300: dt: 0.9000, rms radial error=149.617, avgs=0 150/300: dt: 0.9000, rms radial error=148.771, avgs=0 155/300: dt: 0.9000, rms radial error=147.929, avgs=0 160/300: dt: 0.9000, rms radial error=147.092, avgs=0 165/300: dt: 0.9000, rms radial error=146.260, avgs=0 170/300: dt: 0.9000, rms radial error=145.432, avgs=0 175/300: dt: 0.9000, rms radial error=144.609, avgs=0 180/300: dt: 0.9000, rms radial error=143.791, avgs=0 185/300: dt: 0.9000, rms radial error=142.977, avgs=0 190/300: dt: 0.9000, rms radial error=142.168, avgs=0 195/300: dt: 0.9000, rms radial error=141.364, avgs=0 200/300: dt: 0.9000, rms radial error=140.563, avgs=0 205/300: dt: 0.9000, rms radial error=139.767, avgs=0 210/300: dt: 0.9000, rms radial error=138.976, avgs=0 215/300: dt: 0.9000, rms radial error=138.189, avgs=0 220/300: dt: 0.9000, rms radial error=137.407, avgs=0 225/300: dt: 0.9000, rms radial error=136.629, avgs=0 230/300: dt: 0.9000, rms radial error=135.855, avgs=0 235/300: dt: 0.9000, rms radial error=135.086, avgs=0 240/300: dt: 0.9000, rms radial error=134.322, avgs=0 245/300: dt: 0.9000, rms radial error=133.561, avgs=0 250/300: dt: 0.9000, rms radial error=132.805, avgs=0 255/300: dt: 0.9000, rms radial error=132.053, avgs=0 260/300: dt: 0.9000, rms radial error=131.306, avgs=0 265/300: dt: 0.9000, rms radial error=130.563, avgs=0 270/300: dt: 0.9000, rms radial error=129.824, avgs=0 275/300: dt: 0.9000, rms radial error=129.089, avgs=0 280/300: dt: 0.9000, rms radial error=128.358, avgs=0 285/300: dt: 0.9000, rms radial error=127.632, avgs=0 290/300: dt: 0.9000, rms radial error=126.910, avgs=0 295/300: dt: 0.9000, rms radial error=126.192, avgs=0 300/300: dt: 0.9000, rms radial error=125.478, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 27733.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 5160.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 626.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00305 epoch 4 (K=640.0), pass 1, starting sse = 48.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/10 = 0.00686 final distance error %26.51 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 715.522272 mris_sphere stimesec 8.972901 mris_sphere ru_maxrss 358892 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 3667328 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 15792 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 116174 mris_sphere ru_nivcsw 4036 FSRUNTIME@ mris_sphere 0.0487 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue May 25 21:18:24 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Tue May 25 21:18:24 UTC 2021 mris_fix_topology -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-05 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=-186 (nv=224390, nf=449152, ne=673728, g=94) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 8547 ambiguous faces found in tessellation segmenting defects... 93 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 27 into 30 -merging segment 43 into 37 -merging segment 45 into 42 -merging segment 57 into 42 -merging segment 50 into 47 -merging segment 69 into 62 87 defects to be corrected 0 vertices coincident reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2811 (-4.6405) -vertex loglikelihood: -5.9199 (-2.9600) -normal dot loglikelihood: -3.5383 (-3.5383) -quad curv loglikelihood: -6.3125 (-3.1562) Total Loglikelihood : -25.0518 CORRECTING DEFECT 0 (vertices=22, convex hull=50, v0=8) After retessellation of defect 0 (v0=8), euler #=-85 (219055,654833,435693) : difference with theory (-84) = 1 CORRECTING DEFECT 1 (vertices=20, convex hull=54, v0=1549) After retessellation of defect 1 (v0=1549), euler #=-84 (219061,654871,435726) : difference with theory (-83) = 1 CORRECTING DEFECT 2 (vertices=22, convex hull=24, v0=7386) After retessellation of defect 2 (v0=7386), euler #=-83 (219062,654882,435737) : difference with theory (-82) = 1 CORRECTING DEFECT 3 (vertices=34, convex hull=73, v0=9250) After retessellation of defect 3 (v0=9250), euler #=-82 (219069,654932,435781) : difference with theory (-81) = 1 CORRECTING DEFECT 4 (vertices=69, convex hull=76, v0=9731) After retessellation of defect 4 (v0=9731), euler #=-81 (219077,654987,435829) : difference with theory (-80) = 1 CORRECTING DEFECT 5 (vertices=113, convex hull=116, v0=11406) After retessellation of defect 5 (v0=11406), euler #=-80 (219098,655098,435920) : difference with theory (-79) = 1 CORRECTING DEFECT 6 (vertices=19, convex hull=53, v0=17187) After retessellation of defect 6 (v0=17187), euler #=-79 (219103,655134,435952) : difference with theory (-78) = 1 CORRECTING DEFECT 7 (vertices=13, convex hull=13, v0=20675) After retessellation of defect 7 (v0=20675), euler #=-78 (219104,655141,435959) : difference with theory (-77) = 1 CORRECTING DEFECT 8 (vertices=21, convex hull=60, v0=21985) After retessellation of defect 8 (v0=21985), euler #=-77 (219109,655180,435994) : difference with theory (-76) = 1 CORRECTING DEFECT 9 (vertices=59, convex hull=74, v0=27853) After retessellation of defect 9 (v0=27853), euler #=-76 (219118,655237,436043) : difference with theory (-75) = 1 CORRECTING DEFECT 10 (vertices=251, convex hull=176, v0=36874) After retessellation of defect 10 (v0=36874), euler #=-75 (219146,655410,436189) : difference with theory (-74) = 1 CORRECTING DEFECT 11 (vertices=57, convex hull=21, v0=37649) After retessellation of defect 11 (v0=37649), euler #=-74 (219147,655421,436200) : difference with theory (-73) = 1 CORRECTING DEFECT 12 (vertices=40, convex hull=39, v0=38427) After retessellation of defect 12 (v0=38427), euler #=-73 (219148,655438,436217) : difference with theory (-72) = 1 CORRECTING DEFECT 13 (vertices=6, convex hull=23, v0=43319) After retessellation of defect 13 (v0=43319), euler #=-72 (219149,655447,436226) : difference with theory (-71) = 1 CORRECTING DEFECT 14 (vertices=12, convex hull=27, v0=50524) After retessellation of defect 14 (v0=50524), euler #=-71 (219150,655461,436240) : difference with theory (-70) = 1 CORRECTING DEFECT 15 (vertices=27, convex hull=65, v0=68567) After retessellation of defect 15 (v0=68567), euler #=-70 (219160,655515,436285) : difference with theory (-69) = 1 CORRECTING DEFECT 16 (vertices=16, convex hull=28, v0=69344) After retessellation of defect 16 (v0=69344), euler #=-69 (219164,655535,436302) : difference with theory (-68) = 1 CORRECTING DEFECT 17 (vertices=31, convex hull=66, v0=69630) After retessellation of defect 17 (v0=69630), euler #=-68 (219173,655587,436346) : difference with theory (-67) = 1 CORRECTING DEFECT 18 (vertices=31, convex hull=27, v0=80101) After retessellation of defect 18 (v0=80101), euler #=-67 (219176,655603,436360) : difference with theory (-66) = 1 CORRECTING DEFECT 19 (vertices=30, convex hull=63, v0=86372) After retessellation of defect 19 (v0=86372), euler #=-66 (219186,655660,436408) : difference with theory (-65) = 1 CORRECTING DEFECT 20 (vertices=54, convex hull=57, v0=91238) After retessellation of defect 20 (v0=91238), euler #=-65 (219198,655723,436460) : difference with theory (-64) = 1 CORRECTING DEFECT 21 (vertices=36, convex hull=27, v0=93685) After retessellation of defect 21 (v0=93685), euler #=-64 (219202,655744,436478) : difference with theory (-63) = 1 CORRECTING DEFECT 22 (vertices=13, convex hull=21, v0=93746) After retessellation of defect 22 (v0=93746), euler #=-63 (219203,655753,436487) : difference with theory (-62) = 1 CORRECTING DEFECT 23 (vertices=21, convex hull=42, v0=97006) After retessellation of defect 23 (v0=97006), euler #=-62 (219209,655784,436513) : difference with theory (-61) = 1 CORRECTING DEFECT 24 (vertices=50, convex hull=67, v0=98626) After retessellation of defect 24 (v0=98626), euler #=-61 (219220,655844,436563) : difference with theory (-60) = 1 CORRECTING DEFECT 25 (vertices=33, convex hull=41, v0=98818) After retessellation of defect 25 (v0=98818), euler #=-60 (219228,655886,436598) : difference with theory (-59) = 1 CORRECTING DEFECT 26 (vertices=53, convex hull=72, v0=98949) After retessellation of defect 26 (v0=98949), euler #=-59 (219237,655946,436650) : difference with theory (-58) = 1 CORRECTING DEFECT 27 (vertices=36, convex hull=58, v0=100555) After retessellation of defect 27 (v0=100555), euler #=-58 (219245,655998,436695) : difference with theory (-57) = 1 CORRECTING DEFECT 28 (vertices=74, convex hull=83, v0=101546) After retessellation of defect 28 (v0=101546), euler #=-57 (219254,656062,436751) : difference with theory (-56) = 1 CORRECTING DEFECT 29 (vertices=138, convex hull=98, v0=104332) After retessellation of defect 29 (v0=104332), euler #=-55 (219266,656147,436826) : difference with theory (-55) = 0 CORRECTING DEFECT 30 (vertices=16, convex hull=26, v0=104903) After retessellation of defect 30 (v0=104903), euler #=-54 (219267,656161,436840) : difference with theory (-54) = 0 CORRECTING DEFECT 31 (vertices=38, convex hull=88, v0=105229) After retessellation of defect 31 (v0=105229), euler #=-53 (219280,656240,436907) : difference with theory (-53) = 0 CORRECTING DEFECT 32 (vertices=18, convex hull=34, v0=105910) After retessellation of defect 32 (v0=105910), euler #=-52 (219284,656261,436925) : difference with theory (-52) = 0 CORRECTING DEFECT 33 (vertices=43, convex hull=38, v0=106562) After retessellation of defect 33 (v0=106562), euler #=-51 (219287,656284,436946) : difference with theory (-51) = 0 CORRECTING DEFECT 34 (vertices=95, convex hull=106, v0=106690) After retessellation of defect 34 (v0=106690), euler #=-50 (219297,656362,437015) : difference with theory (-50) = 0 CORRECTING DEFECT 35 (vertices=8, convex hull=26, v0=107558) After retessellation of defect 35 (v0=107558), euler #=-49 (219299,656377,437029) : difference with theory (-49) = 0 CORRECTING DEFECT 36 (vertices=296, convex hull=196, v0=116423) After retessellation of defect 36 (v0=116423), euler #=-47 (219336,656596,437213) : difference with theory (-48) = -1 CORRECTING DEFECT 37 (vertices=106, convex hull=62, v0=116633) After retessellation of defect 37 (v0=116633), euler #=-46 (219340,656635,437249) : difference with theory (-47) = -1 CORRECTING DEFECT 38 (vertices=188, convex hull=64, v0=118215) After retessellation of defect 38 (v0=118215), euler #=-45 (219349,656693,437299) : difference with theory (-46) = -1 CORRECTING DEFECT 39 (vertices=28, convex hull=55, v0=121151) After retessellation of defect 39 (v0=121151), euler #=-44 (219358,656740,437338) : difference with theory (-45) = -1 CORRECTING DEFECT 40 (vertices=25, convex hull=49, v0=122129) After retessellation of defect 40 (v0=122129), euler #=-43 (219364,656777,437370) : difference with theory (-44) = -1 CORRECTING DEFECT 41 (vertices=950, convex hull=584, v0=128769) L defect detected... After retessellation of defect 41 (v0=128769), euler #=-44 (219578,657745,438123) : difference with theory (-43) = 1 CORRECTING DEFECT 42 (vertices=38, convex hull=73, v0=132174) After retessellation of defect 42 (v0=132174), euler #=-43 (219586,657798,438169) : difference with theory (-42) = 1 CORRECTING DEFECT 43 (vertices=31, convex hull=19, v0=136639) After retessellation of defect 43 (v0=136639), euler #=-42 (219589,657812,438181) : difference with theory (-41) = 1 CORRECTING DEFECT 44 (vertices=92, convex hull=137, v0=139652) After retessellation of defect 44 (v0=139652), euler #=-40 (219606,657937,438291) : difference with theory (-40) = 0 CORRECTING DEFECT 45 (vertices=20, convex hull=19, v0=140071) After retessellation of defect 45 (v0=140071), euler #=-39 (219607,657944,438298) : difference with theory (-39) = 0 CORRECTING DEFECT 46 (vertices=8, convex hull=18, v0=144117) After retessellation of defect 46 (v0=144117), euler #=-38 (219608,657950,438304) : difference with theory (-38) = 0 CORRECTING DEFECT 47 (vertices=37, convex hull=48, v0=145878) After retessellation of defect 47 (v0=145878), euler #=-37 (219615,657987,438335) : difference with theory (-37) = 0 CORRECTING DEFECT 48 (vertices=13, convex hull=32, v0=146751) After retessellation of defect 48 (v0=146751), euler #=-36 (219618,658003,438349) : difference with theory (-36) = 0 CORRECTING DEFECT 49 (vertices=29, convex hull=24, v0=147843) After retessellation of defect 49 (v0=147843), euler #=-35 (219622,658020,438363) : difference with theory (-35) = 0 CORRECTING DEFECT 50 (vertices=39, convex hull=23, v0=148041) After retessellation of defect 50 (v0=148041), euler #=-34 (219624,658029,438371) : difference with theory (-34) = 0 CORRECTING DEFECT 51 (vertices=123, convex hull=98, v0=149460) After retessellation of defect 51 (v0=149460), euler #=-33 (219636,658112,438443) : difference with theory (-33) = 0 CORRECTING DEFECT 52 (vertices=441, convex hull=343, v0=150839) After retessellation of defect 52 (v0=150839), euler #=-32 (219726,658571,438813) : difference with theory (-32) = 0 CORRECTING DEFECT 53 (vertices=16, convex hull=30, v0=160317) After retessellation of defect 53 (v0=160317), euler #=-31 (219728,658588,438829) : difference with theory (-31) = 0 CORRECTING DEFECT 54 (vertices=31, convex hull=59, v0=160377) After retessellation of defect 54 (v0=160377), euler #=-30 (219737,658638,438871) : difference with theory (-30) = 0 CORRECTING DEFECT 55 (vertices=25, convex hull=66, v0=162472) After retessellation of defect 55 (v0=162472), euler #=-29 (219744,658685,438912) : difference with theory (-29) = 0 CORRECTING DEFECT 56 (vertices=12, convex hull=23, v0=163138) After retessellation of defect 56 (v0=163138), euler #=-28 (219746,658699,438925) : difference with theory (-28) = 0 CORRECTING DEFECT 57 (vertices=25, convex hull=55, v0=163261) After retessellation of defect 57 (v0=163261), euler #=-26 (219752,658737,438959) : difference with theory (-27) = -1 CORRECTING DEFECT 58 (vertices=152, convex hull=50, v0=164156) After retessellation of defect 58 (v0=164156), euler #=-25 (219761,658784,438998) : difference with theory (-26) = -1 CORRECTING DEFECT 59 (vertices=74, convex hull=58, v0=164255) After retessellation of defect 59 (v0=164255), euler #=-24 (219770,658833,439039) : difference with theory (-25) = -1 CORRECTING DEFECT 60 (vertices=19, convex hull=20, v0=164840) After retessellation of defect 60 (v0=164840), euler #=-24 (219771,658846,439051) : difference with theory (-24) = 0 CORRECTING DEFECT 61 (vertices=33, convex hull=23, v0=165203) After retessellation of defect 61 (v0=165203), euler #=-23 (219774,658861,439064) : difference with theory (-23) = 0 CORRECTING DEFECT 62 (vertices=23, convex hull=21, v0=165456) After retessellation of defect 62 (v0=165456), euler #=-22 (219778,658880,439080) : difference with theory (-22) = 0 CORRECTING DEFECT 63 (vertices=8, convex hull=43, v0=166836) After retessellation of defect 63 (v0=166836), euler #=-21 (219781,658901,439099) : difference with theory (-21) = 0 CORRECTING DEFECT 64 (vertices=8, convex hull=29, v0=168329) After retessellation of defect 64 (v0=168329), euler #=-20 (219782,658911,439109) : difference with theory (-20) = 0 CORRECTING DEFECT 65 (vertices=177, convex hull=130, v0=169508) After retessellation of defect 65 (v0=169508), euler #=-19 (219795,659016,439202) : difference with theory (-19) = 0 CORRECTING DEFECT 66 (vertices=23, convex hull=61, v0=171128) After retessellation of defect 66 (v0=171128), euler #=-18 (219800,659052,439234) : difference with theory (-18) = 0 CORRECTING DEFECT 67 (vertices=42, convex hull=59, v0=172140) After retessellation of defect 67 (v0=172140), euler #=-17 (219814,659117,439286) : difference with theory (-17) = 0 CORRECTING DEFECT 68 (vertices=5, convex hull=25, v0=172254) After retessellation of defect 68 (v0=172254), euler #=-16 (219815,659125,439294) : difference with theory (-16) = 0 CORRECTING DEFECT 69 (vertices=12, convex hull=22, v0=172443) After retessellation of defect 69 (v0=172443), euler #=-15 (219817,659137,439305) : difference with theory (-15) = 0 CORRECTING DEFECT 70 (vertices=29, convex hull=48, v0=172538) After retessellation of defect 70 (v0=172538), euler #=-14 (219825,659178,439339) : difference with theory (-14) = 0 CORRECTING DEFECT 71 (vertices=10, convex hull=15, v0=173311) After retessellation of defect 71 (v0=173311), euler #=-13 (219828,659191,439350) : difference with theory (-13) = 0 CORRECTING DEFECT 72 (vertices=17, convex hull=25, v0=180142) After retessellation of defect 72 (v0=180142), euler #=-12 (219830,659204,439362) : difference with theory (-12) = 0 CORRECTING DEFECT 73 (vertices=22, convex hull=29, v0=181123) After retessellation of defect 73 (v0=181123), euler #=-11 (219833,659222,439378) : difference with theory (-11) = 0 CORRECTING DEFECT 74 (vertices=50, convex hull=77, v0=183284) After retessellation of defect 74 (v0=183284), euler #=-10 (219839,659271,439422) : difference with theory (-10) = 0 CORRECTING DEFECT 75 (vertices=36, convex hull=64, v0=184143) After retessellation of defect 75 (v0=184143), euler #=-9 (219848,659327,439470) : difference with theory (-9) = 0 CORRECTING DEFECT 76 (vertices=74, convex hull=34, v0=187798) After retessellation of defect 76 (v0=187798), euler #=-8 (219857,659365,439500) : difference with theory (-8) = 0 CORRECTING DEFECT 77 (vertices=5, convex hull=13, v0=189942) After retessellation of defect 77 (v0=189942), euler #=-7 (219858,659370,439505) : difference with theory (-7) = 0 CORRECTING DEFECT 78 (vertices=70, convex hull=86, v0=193170) After retessellation of defect 78 (v0=193170), euler #=-6 (219867,659432,439559) : difference with theory (-6) = 0 CORRECTING DEFECT 79 (vertices=100, convex hull=107, v0=207155) After retessellation of defect 79 (v0=207155), euler #=-5 (219881,659525,439639) : difference with theory (-5) = 0 CORRECTING DEFECT 80 (vertices=43, convex hull=57, v0=211932) After retessellation of defect 80 (v0=211932), euler #=-4 (219885,659561,439672) : difference with theory (-4) = 0 CORRECTING DEFECT 81 (vertices=44, convex hull=68, v0=214444) After retessellation of defect 81 (v0=214444), euler #=-3 (219898,659631,439730) : difference with theory (-3) = 0 CORRECTING DEFECT 82 (vertices=16, convex hull=49, v0=216590) After retessellation of defect 82 (v0=216590), euler #=-2 (219902,659657,439753) : difference with theory (-2) = 0 CORRECTING DEFECT 83 (vertices=10, convex hull=17, v0=216941) After retessellation of defect 83 (v0=216941), euler #=-1 (219902,659661,439758) : difference with theory (-1) = 0 CORRECTING DEFECT 84 (vertices=33, convex hull=71, v0=218060) After retessellation of defect 84 (v0=218060), euler #=0 (219912,659718,439806) : difference with theory (0) = 0 CORRECTING DEFECT 85 (vertices=6, convex hull=22, v0=221526) After retessellation of defect 85 (v0=221526), euler #=1 (219912,659724,439813) : difference with theory (1) = 0 CORRECTING DEFECT 86 (vertices=6, convex hull=17, v0=223767) After retessellation of defect 86 (v0=223767), euler #=2 (219913,659733,439822) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.71 +- 0.19 (0.05-->7.39) (max @ vno 41204 --> 55581) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.71 +- 0.19 (0.05-->7.39) (max @ vno 41204 --> 55581) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 307 mutations (37.2%), 518 crossovers (62.8%), 120 vertices were eliminated building final representation... 4477 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=219913, nf=439822, ne=659733, g=0) writing corrected surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 42.9 minutes 0 defective edges removing intersecting faces 000: 547 intersecting 001: 25 intersecting 002: 9 intersecting expanding nbhd size to 2 003: 17 intersecting 004: 2 intersecting mris_fix_topology utimesec 2579.959836 mris_fix_topology stimesec 3.329158 mris_fix_topology ru_maxrss 728976 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 4090427 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 20744 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5444 mris_fix_topology ru_nivcsw 913 FSRUNTIME@ mris_fix_topology lh 0.7147 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 219913 - 659733 + 439822 = 2 --> 0 holes F =2V-4: 439822 = 439826-4 (0) 2E=3F: 1319466 = 1319466 (0) total defect index = 0 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 90 intersecting 001: 9 intersecting 002: 8 intersecting 003: 7 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue May 25 22:01:27 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... 43249 bright wm thresholded. 3 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.orig... computing class statistics... border white: 444408 voxels (1.36%) border gray 456912 voxels (1.39%) WM (103.0): 102.4 +- 6.3 [70.0 --> 110.0] GM (83.0) : 81.8 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.0 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.0 (was 40) setting MAX_GRAY to 101.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.67 +- 0.18 (0.01-->4.02) (max @ vno 52852 --> 219127) face area 0.19 +- 0.08 (0.00-->1.84) mean absolute distance = 1.45 +- 1.55 7410 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=108+-3.5, GM=78+-7.0 mean inside = 100.5, mean outside = 83.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=95.2, 161 (161) missing vertices, mean dist -0.7 [2.1 (%50.2)->0.6 (%49.8))] %42 local maxima, %43 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg43, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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 0.71 +- 0.19 (0.05-->4.08) (max @ vno 52852 --> 219127) face area 0.19 +- 0.08 (0.00-->2.33) mean absolute distance = 0.59 +- 0.79 7066 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4686806.0, rms=9.374 001: dt: 0.5000, sse=2312558.8, rms=5.728 (38.889%) 002: dt: 0.5000, sse=1490072.1, rms=3.650 (36.283%) 003: dt: 0.5000, sse=1318963.2, rms=3.038 (16.756%) 004: dt: 0.5000, sse=1306999.0, rms=2.921 (3.877%) rms = 2.89, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=1286356.9, rms=2.886 (1.201%) 006: dt: 0.2500, sse=1070838.4, rms=1.718 (40.455%) 007: dt: 0.2500, sse=1035940.1, rms=1.416 (17.600%) 008: dt: 0.2500, sse=1024632.2, rms=1.324 (6.453%) 009: dt: 0.2500, sse=1022444.4, rms=1.260 (4.858%) rms = 1.23, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=1010951.4, rms=1.226 (2.736%) rms = 1.19, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=1009374.2, rms=1.193 (2.683%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=94.5, 218 (49) missing vertices, mean dist -0.2 [0.9 (%40.3)->0.3 (%59.7))] %81 local maxima, %11 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg43, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.70 +- 0.19 (0.01-->4.01) (max @ vno 52852 --> 219127) face area 0.21 +- 0.10 (0.00-->2.74) mean absolute distance = 0.33 +- 0.57 8848 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1856631.6, rms=4.331 012: dt: 0.5000, sse=1411754.5, rms=2.759 (36.288%) 013: dt: 0.5000, sse=1380191.4, rms=2.686 (2.663%) rms = 2.87, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=1177384.6, rms=1.749 (34.862%) 015: dt: 0.2500, sse=1124675.5, rms=1.243 (28.959%) 016: dt: 0.2500, sse=1123379.2, rms=1.118 (10.033%) rms = 1.07, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=1118806.9, rms=1.071 (4.187%) rms = 1.03, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=1111210.6, rms=1.030 (3.897%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.6, 218 (27) missing vertices, mean dist -0.1 [0.6 (%38.6)->0.2 (%61.4))] %90 local maxima, % 4 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg43, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.70 +- 0.19 (0.02-->3.98) (max @ vno 52852 --> 219127) face area 0.20 +- 0.09 (0.00-->2.66) mean absolute distance = 0.24 +- 0.44 6564 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1249999.9, rms=2.270 019: dt: 0.5000, sse=1241216.9, rms=2.037 (10.296%) rms = 2.39, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=1104341.2, rms=1.343 (34.058%) 021: dt: 0.2500, sse=1112875.9, rms=1.050 (21.816%) 022: dt: 0.2500, sse=1129231.6, rms=0.989 (5.788%) rms = 0.97, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=1068375.0, rms=0.966 (2.359%) rms = 0.93, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=1058996.5, rms=0.932 (3.491%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.4, 255 (21) missing vertices, mean dist -0.0 [0.4 (%32.4)->0.1 (%67.6))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg43, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1119626.5, rms=1.542 025: dt: 0.5000, sse=1120578.8, rms=1.443 (6.452%) rms = 1.92, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=1054367.6, rms=0.942 (34.724%) 027: dt: 0.2500, sse=1060889.4, rms=0.821 (12.802%) rms = 0.79, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=1039580.2, rms=0.787 (4.203%) rms = 0.76, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=1039679.5, rms=0.760 (3.406%) positioning took 0.8 minutes generating cortex label... 15 non-cortical segments detected only using segment with 12302 vertices erasing segment 0 (vno[0] = 35069) erasing segment 2 (vno[0] = 142384) erasing segment 3 (vno[0] = 145013) erasing segment 4 (vno[0] = 162126) erasing segment 5 (vno[0] = 163359) erasing segment 6 (vno[0] = 164494) erasing segment 7 (vno[0] = 165603) erasing segment 8 (vno[0] = 166970) erasing segment 9 (vno[0] = 167919) erasing segment 10 (vno[0] = 169073) erasing segment 11 (vno[0] = 170252) erasing segment 12 (vno[0] = 171382) erasing segment 13 (vno[0] = 171392) erasing segment 14 (vno[0] = 172355) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.area vertex spacing 0.70 +- 0.19 (0.02-->3.88) (max @ vno 52852 --> 219127) face area 0.20 +- 0.09 (0.00-->2.65) refinement took 6.2 minutes #-------------------------------------------- #@# Smooth2 lh Tue May 25 22:07:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts 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... #-------------------------------------------- #@# Inflation2 lh Tue May 25 22:07:46 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_inflate -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated niterations = 50 Reading ../surf/lh.smoothwm avg radius = 47.8 mm, total surface area = 83000 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.155 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) step 065: RMS=0.021 (target=0.015) step 070: RMS=0.021 (target=0.015) step 075: RMS=0.020 (target=0.015) step 080: RMS=0.019 (target=0.015) step 085: RMS=0.019 (target=0.015) step 090: RMS=0.018 (target=0.015) step 095: RMS=0.018 (target=0.015) step 100: RMS=0.017 (target=0.015) step 105: RMS=0.017 (target=0.015) step 110: RMS=0.017 (target=0.015) step 115: RMS=0.017 (target=0.015) step 120: RMS=0.017 (target=0.015) step 125: RMS=0.016 (target=0.015) step 130: RMS=0.016 (target=0.015) step 135: RMS=0.016 (target=0.015) step 140: RMS=0.016 (target=0.015) step 145: RMS=0.016 (target=0.015) step 150: RMS=0.016 (target=0.015) step 155: RMS=0.016 (target=0.015) step 160: RMS=0.016 (target=0.015) step 165: RMS=0.016 (target=0.015) step 170: RMS=0.016 (target=0.015) step 175: RMS=0.015 (target=0.015) step 180: RMS=0.015 (target=0.015) step 185: RMS=0.015 (target=0.015) step 190: RMS=0.015 (target=0.015) step 195: RMS=0.015 (target=0.015) step 200: RMS=0.015 (target=0.015) step 205: RMS=0.015 (target=0.015) step 210: RMS=0.015 (target=0.015) step 215: RMS=0.015 (target=0.015) step 220: RMS=0.015 (target=0.015) inflation complete. inflation took 1.6 minutes mris_inflate utimesec 491.015536 mris_inflate stimesec 8.816853 mris_inflate ru_maxrss 351672 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 3539311 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 17192 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 140840 mris_inflate ru_nivcsw 3143 #-------------------------------------------- #@# Curv .H and .K lh Tue May 25 22:09:21 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf mris_curvature -w lh.white.preaparc total integrated curvature = 42.573*4pi (534.989) --> -42 handles ICI = 256.5, FI = 2624.2, variation=40836.123 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 345 vertices thresholded to be in k1 ~ [-0.15 0.69], k2 ~ [-0.11 0.05] total integrated curvature = 0.735*4pi (9.233) --> 0 handles ICI = 1.2, FI = 4.1, variation=82.318 210 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 251 vertices thresholded to be in [-0.11 0.07] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.014 done. #----------------------------------------- #@# Curvature Stats lh Tue May 25 22:11:04 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-05 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 [ sub-05/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 [ 414 ] Gb_filter = 0 WARN: S lookup min: -0.357876 WARN: S explicit min: 0.000000 vertex = 405 #-------------------------------------------- #@# Sphere lh Tue May 25 22:11:10 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_sphere -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 = 8 == scaling brain by 0.296... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=blg43, 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 %38.10 pass 1: epoch 2 of 3 starting distance error %21.34 unfolding complete - removing small folds... starting distance error %21.16 removing remaining folds... final distance error %21.17 MRISunfold() return, current seed 1234 -01: dt=0.0000, 545 negative triangles 098: dt=0.9900, 545 negative triangles 099: dt=0.9900, 339 negative triangles 100: dt=0.9900, 271 negative triangles 101: dt=0.9900, 243 negative triangles 102: dt=0.9900, 232 negative triangles 103: dt=0.9900, 219 negative triangles 104: dt=0.9900, 215 negative triangles 105: dt=0.9900, 210 negative triangles 106: dt=0.9900, 201 negative triangles 107: dt=0.9900, 190 negative triangles 108: dt=0.9900, 202 negative triangles 109: dt=0.9900, 191 negative triangles 110: dt=0.9900, 184 negative triangles 111: dt=0.9900, 183 negative triangles 112: dt=0.9900, 174 negative triangles 113: dt=0.9900, 175 negative triangles 114: dt=0.9900, 162 negative triangles 115: dt=0.9900, 162 negative triangles 116: dt=0.9900, 161 negative triangles 117: dt=0.9900, 157 negative triangles 118: dt=0.9900, 160 negative triangles 119: dt=0.9900, 159 negative triangles 120: dt=0.9900, 155 negative triangles 121: dt=0.9900, 165 negative triangles 122: dt=0.9900, 144 negative triangles 123: dt=0.9900, 148 negative triangles 124: dt=0.9900, 143 negative triangles 125: dt=0.9900, 156 negative triangles 126: dt=0.9900, 143 negative triangles 127: dt=0.9900, 147 negative triangles 128: dt=0.9900, 141 negative triangles 129: dt=0.9900, 134 negative triangles 130: dt=0.9900, 142 negative triangles 131: dt=0.9900, 144 negative triangles 132: dt=0.9900, 153 negative triangles 133: dt=0.9900, 142 negative triangles 134: dt=0.9900, 131 negative triangles 135: dt=0.9900, 132 negative triangles 136: dt=0.9900, 117 negative triangles 137: dt=0.9900, 133 negative triangles 138: dt=0.9900, 124 negative triangles 139: dt=0.9900, 133 negative triangles 140: dt=0.9900, 128 negative triangles 141: dt=0.9900, 126 negative triangles 142: dt=0.9900, 126 negative triangles 143: dt=0.9900, 121 negative triangles 144: dt=0.9900, 118 negative triangles 145: dt=0.9900, 119 negative triangles 146: dt=0.9900, 112 negative triangles 147: dt=0.9900, 108 negative triangles 148: dt=0.9900, 112 negative triangles 149: dt=0.9900, 110 negative triangles 150: dt=0.9900, 103 negative triangles 151: dt=0.9900, 95 negative triangles 152: dt=0.9900, 91 negative triangles 153: dt=0.9900, 94 negative triangles 154: dt=0.9900, 82 negative triangles 155: dt=0.9900, 94 negative triangles 156: dt=0.9900, 84 negative triangles 157: dt=0.9900, 90 negative triangles 158: dt=0.9900, 83 negative triangles 159: dt=0.9900, 82 negative triangles 160: dt=0.9900, 78 negative triangles 161: dt=0.9900, 84 negative triangles 162: dt=0.9900, 76 negative triangles 163: dt=0.9900, 76 negative triangles 164: dt=0.9900, 76 negative triangles 165: dt=0.9900, 83 negative triangles 166: dt=0.9900, 79 negative triangles 167: dt=0.9900, 85 negative triangles 168: dt=0.9900, 81 negative triangles 169: dt=0.9900, 83 negative triangles 170: dt=0.9900, 74 negative triangles 171: dt=0.9900, 82 negative triangles 172: dt=0.9900, 78 negative triangles 173: dt=0.9900, 75 negative triangles 174: dt=0.9900, 78 negative triangles 175: dt=0.9900, 71 negative triangles 176: dt=0.9900, 78 negative triangles 177: dt=0.9900, 76 negative triangles 178: dt=0.9900, 69 negative triangles 179: dt=0.9900, 65 negative triangles 180: dt=0.9900, 48 negative triangles 181: dt=0.9900, 67 negative triangles 182: dt=0.9900, 51 negative triangles 183: dt=0.9900, 59 negative triangles 184: dt=0.9900, 59 negative triangles 185: dt=0.9900, 62 negative triangles 186: dt=0.9900, 53 negative triangles 187: dt=0.9900, 52 negative triangles 188: dt=0.9900, 50 negative triangles 189: dt=0.9900, 58 negative triangles 190: dt=0.9405, 57 negative triangles 191: dt=0.9405, 45 negative triangles 192: dt=0.9405, 42 negative triangles 193: dt=0.9405, 47 negative triangles 194: dt=0.9405, 44 negative triangles 195: dt=0.9405, 50 negative triangles 196: dt=0.9405, 41 negative triangles 197: dt=0.9405, 49 negative triangles 198: dt=0.9405, 42 negative triangles 199: dt=0.9405, 45 negative triangles 200: dt=0.9405, 40 negative triangles 201: dt=0.9405, 42 negative triangles 202: dt=0.9405, 41 negative triangles 203: dt=0.9405, 40 negative triangles 204: dt=0.9405, 41 negative triangles 205: dt=0.9405, 41 negative triangles 206: dt=0.9405, 35 negative triangles 207: dt=0.9405, 38 negative triangles 208: dt=0.9405, 37 negative triangles 209: dt=0.9405, 35 negative triangles 210: dt=0.9405, 31 negative triangles 211: dt=0.9405, 29 negative triangles 212: dt=0.9405, 28 negative triangles 213: dt=0.9405, 29 negative triangles 214: dt=0.9405, 21 negative triangles 215: dt=0.9405, 28 negative triangles 216: dt=0.9405, 25 negative triangles 217: dt=0.9405, 26 negative triangles 218: dt=0.9405, 24 negative triangles 219: dt=0.9405, 28 negative triangles 220: dt=0.9405, 31 negative triangles 221: dt=0.9405, 27 negative triangles 222: dt=0.9405, 22 negative triangles 223: dt=0.9405, 23 negative triangles 224: dt=0.9405, 20 negative triangles 225: dt=0.9405, 24 negative triangles 226: dt=0.9405, 19 negative triangles 227: dt=0.9405, 20 negative triangles 228: dt=0.9405, 20 negative triangles 229: dt=0.9405, 19 negative triangles 230: dt=0.9405, 18 negative triangles 231: dt=0.9405, 13 negative triangles 232: dt=0.9405, 17 negative triangles 233: dt=0.9405, 17 negative triangles 234: dt=0.9405, 10 negative triangles 235: dt=0.9405, 7 negative triangles 236: dt=0.9405, 15 negative triangles 237: dt=0.9405, 6 negative triangles 238: dt=0.9405, 7 negative triangles 239: dt=0.9405, 5 negative triangles 240: dt=0.9405, 8 negative triangles 241: dt=0.9405, 3 negative triangles 242: dt=0.9405, 3 negative triangles 243: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.17 hours mris_sphere utimesec 4028.485169 mris_sphere stimesec 39.519588 mris_sphere ru_maxrss 476512 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 24002320 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 15472 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 139819 mris_sphere ru_nivcsw 13898 FSRUNTIME@ mris_sphere 0.1726 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue May 25 22:21:32 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts cmdline mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/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 /opt/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=blg43, 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=blg43, 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 = 6.826 curvature mean = 0.024, std = 0.820 curvature mean = 0.016, std = 0.904 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 438496.5, tmin=1.1885 d=32.00 min @ (8.00, 8.00, 0.00) sse = 319046.1, tmin=2.4091 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 308307.8, tmin=4.7467 d=4.00 min @ (1.00, 0.00, 0.00) sse = 306741.2, tmin=5.8988 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 306634.7, tmin=7.0472 d=1.00 min @ (0.25, 0.00, 0.25) sse = 306444.0, tmin=8.1960 d=0.50 min @ (0.00, 0.12, -0.12) sse = 306397.1, tmin=9.3614 tol=1.0e+00, sigma=0.5, host=blg43, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.36 min curvature mean = -0.004, std = 0.860 curvature mean = 0.007, std = 0.960 curvature mean = -0.011, std = 0.870 curvature mean = 0.003, std = 0.984 curvature mean = -0.013, std = 0.872 curvature mean = 0.001, std = 0.994 2 Reading smoothwm curvature mean = -0.034, std = 0.379 curvature mean = 0.036, std = 0.243 curvature mean = 0.044, std = 0.281 curvature mean = 0.034, std = 0.297 curvature mean = 0.021, std = 0.440 curvature mean = 0.034, std = 0.323 curvature mean = 0.011, std = 0.566 curvature mean = 0.035, std = 0.332 curvature mean = 0.004, std = 0.667 MRISregister() return, current seed 0 -01: dt=0.0000, 159 negative triangles 116: dt=0.9900, 159 negative triangles expanding nbhd size to 1 117: dt=0.9900, 201 negative triangles 118: dt=0.9900, 163 negative triangles 119: dt=0.9900, 158 negative triangles 120: dt=0.9900, 165 negative triangles 121: dt=0.9900, 158 negative triangles 122: dt=0.9900, 158 negative triangles 123: dt=0.9900, 150 negative triangles 124: dt=0.9900, 143 negative triangles 125: dt=0.9900, 136 negative triangles 126: dt=0.9900, 141 negative triangles 127: dt=0.9900, 133 negative triangles 128: dt=0.9900, 130 negative triangles 129: dt=0.9900, 121 negative triangles 130: dt=0.9900, 126 negative triangles 131: dt=0.9900, 119 negative triangles 132: dt=0.9900, 114 negative triangles 133: dt=0.9900, 114 negative triangles 134: dt=0.9900, 108 negative triangles 135: dt=0.9900, 110 negative triangles 136: dt=0.9900, 108 negative triangles 137: dt=0.9900, 105 negative triangles 138: dt=0.9900, 107 negative triangles 139: dt=0.9900, 107 negative triangles 140: dt=0.9900, 113 negative triangles 141: dt=0.9900, 103 negative triangles 142: dt=0.9900, 99 negative triangles 143: dt=0.9900, 94 negative triangles 144: dt=0.9900, 100 negative triangles 145: dt=0.9900, 99 negative triangles 146: dt=0.9900, 97 negative triangles 147: dt=0.9900, 101 negative triangles 148: dt=0.9900, 98 negative triangles 149: dt=0.9900, 93 negative triangles 150: dt=0.9900, 98 negative triangles 151: dt=0.9900, 89 negative triangles 152: dt=0.9900, 85 negative triangles 153: dt=0.9900, 86 negative triangles 154: dt=0.9900, 87 negative triangles 155: dt=0.9900, 83 negative triangles 156: dt=0.9900, 86 negative triangles 157: dt=0.9900, 84 negative triangles 158: dt=0.9900, 83 negative triangles 159: dt=0.9900, 83 negative triangles 160: dt=0.9900, 81 negative triangles 161: dt=0.9900, 72 negative triangles 162: dt=0.9900, 70 negative triangles 163: dt=0.9900, 66 negative triangles 164: dt=0.9900, 62 negative triangles 165: dt=0.9900, 54 negative triangles 166: dt=0.9900, 54 negative triangles 167: dt=0.9900, 46 negative triangles 168: dt=0.9900, 45 negative triangles 169: dt=0.9900, 39 negative triangles 170: dt=0.9900, 42 negative triangles 171: dt=0.9900, 38 negative triangles 172: dt=0.9900, 37 negative triangles 173: dt=0.9900, 37 negative triangles 174: dt=0.9900, 34 negative triangles 175: dt=0.9900, 32 negative triangles 176: dt=0.9900, 30 negative triangles 177: dt=0.9900, 27 negative triangles 178: dt=0.9900, 27 negative triangles 179: dt=0.9900, 24 negative triangles 180: dt=0.9900, 25 negative triangles 181: dt=0.9900, 22 negative triangles 182: dt=0.9900, 23 negative triangles 183: dt=0.9900, 20 negative triangles 184: dt=0.9900, 23 negative triangles 185: dt=0.9900, 19 negative triangles 186: dt=0.9900, 23 negative triangles 187: dt=0.9900, 19 negative triangles 188: dt=0.9900, 15 negative triangles 189: dt=0.9900, 15 negative triangles 190: dt=0.9900, 13 negative triangles 191: dt=0.9900, 8 negative triangles 192: dt=0.9900, 10 negative triangles 193: dt=0.9900, 8 negative triangles 194: dt=0.9900, 7 negative triangles 195: dt=0.9900, 6 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 8 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 3 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 2 negative triangles 202: dt=0.9900, 3 negative triangles 203: dt=0.9900, 2 negative triangles 204: dt=0.9900, 1 negative triangles 205: dt=0.9900, 2 negative triangles 206: dt=0.9900, 1 negative triangles 207: dt=0.9900, 3 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.53 hours mris_register utimesec 8915.260648 mris_register stimesec 33.737755 mris_register ru_maxrss 400948 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 12844966 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5580 mris_register ru_oublock 15472 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 182134 mris_register ru_nivcsw 39175 FSRUNTIME@ mris_register 0.5335 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue May 25 22:53:33 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts 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 #-------------------------------------------- #@# AvgCurv lh Tue May 25 22:53:36 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mrisp_paint -a 5 /opt/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 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue May 25 22:53:38 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/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 /opt/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... 2207 labels changed using aseg relabeling using gibbs priors... 000: 4609 changed, 219913 examined... 001: 1091 changed, 19120 examined... 002: 292 changed, 5956 examined... 003: 112 changed, 1703 examined... 004: 35 changed, 657 examined... 005: 18 changed, 223 examined... 006: 8 changed, 107 examined... 007: 3 changed, 40 examined... 008: 2 changed, 21 examined... 009: 1 changed, 9 examined... 010: 1 changed, 7 examined... 011: 0 changed, 9 examined... 254 labels changed using aseg 000: 172 total segments, 128 labels (875 vertices) changed 001: 44 total segments, 2 labels (7 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2368 vertices marked for relabeling... 2368 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 18 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue May 25 22:53:56 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... 43249 bright wm thresholded. 3 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.orig... computing class statistics... border white: 444408 voxels (1.36%) border gray 456912 voxels (1.39%) WM (103.0): 102.4 +- 6.3 [70.0 --> 110.0] GM (83.0) : 81.8 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.0 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.0 (was 40) setting MAX_GRAY to 101.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.0 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=108+-3.5, GM=78+-7.0 mean inside = 100.5, mean outside = 83.4 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 0.70 +- 0.19 (0.02-->3.88) (max @ vno 52852 --> 219127) face area 0.20 +- 0.09 (0.00-->2.66) mean absolute distance = 1.33 +- 1.42 7102 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 50 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 668 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown deleting segment 8 with 35 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown mean border=95.1, 217 (215) missing vertices, mean dist -0.5 [2.4 (%38.5)->0.6 (%61.5))] %41 local maxima, %43 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg43, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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 0.71 +- 0.19 (0.02-->4.06) (max @ vno 52852 --> 219127) face area 0.20 +- 0.09 (0.00-->2.25) mean absolute distance = 0.57 +- 0.79 6798 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2354794.5, rms=5.631 001: dt: 0.5000, sse=1433776.8, rms=3.095 (45.043%) 002: dt: 0.5000, sse=1317734.8, rms=2.641 (14.667%) rms = 2.69, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=1163715.0, rms=1.838 (30.405%) 004: dt: 0.2500, sse=1108982.0, rms=1.396 (24.063%) 005: dt: 0.2500, sse=1106921.8, rms=1.302 (6.735%) rms = 1.26, time step reduction 2 of 3 to 0.125... 006: dt: 0.2500, sse=1099793.2, rms=1.260 (3.163%) rms = 1.23, time step reduction 3 of 3 to 0.062... 007: dt: 0.1250, sse=1086808.8, rms=1.228 (2.605%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 1 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 618 points - only 0.00% unknown deleting segment 4 with 39 points - only 0.00% unknown mean border=94.5, 181 (67) missing vertices, mean dist -0.2 [0.9 (%40.0)->0.3 (%60.0))] %81 local maxima, %11 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg43, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.70 +- 0.19 (0.03-->4.17) (max @ vno 52852 --> 219127) face area 0.21 +- 0.10 (0.00-->2.69) mean absolute distance = 0.32 +- 0.56 8748 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1793423.9, rms=4.183 008: dt: 0.5000, sse=1390469.9, rms=2.684 (35.829%) rms = 2.65, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=1351257.5, rms=2.651 (1.225%) 010: dt: 0.2500, sse=1165252.5, rms=1.441 (45.647%) 011: dt: 0.2500, sse=1121417.2, rms=1.189 (17.484%) 012: dt: 0.2500, sse=1131747.2, rms=1.133 (4.713%) rms = 1.10, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=1114557.1, rms=1.103 (2.668%) rms = 1.07, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=1107576.5, rms=1.074 (2.579%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 1 with 42 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 563 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 32 points - only 0.00% unknown deleting segment 8 with 39 points - only 53.85% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown mean border=94.6, 229 (35) missing vertices, mean dist -0.1 [0.5 (%38.5)->0.2 (%61.5))] %90 local maxima, % 4 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg43, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.70 +- 0.19 (0.05-->4.07) (max @ vno 52852 --> 219127) face area 0.20 +- 0.10 (0.00-->2.66) mean absolute distance = 0.24 +- 0.43 6418 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1243448.2, rms=2.283 015: dt: 0.5000, sse=1212723.8, rms=2.043 (10.522%) rms = 2.38, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=1096745.4, rms=1.344 (34.189%) 017: dt: 0.2500, sse=1085591.1, rms=1.044 (22.346%) 018: dt: 0.2500, sse=1062301.1, rms=0.983 (5.806%) rms = 0.96, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=1058492.8, rms=0.959 (2.526%) rms = 0.92, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=1066373.0, rms=0.921 (3.927%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 1 with 57 points - only 0.00% unknown deleting segment 2 with 448 points - only 0.00% unknown deleting segment 3 with 58 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown mean border=94.4, 234 (21) missing vertices, mean dist -0.0 [0.4 (%32.3)->0.1 (%67.7))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg43, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1121547.4, rms=1.501 021: dt: 0.5000, sse=1108986.1, rms=1.408 (6.182%) rms = 1.91, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=1053556.0, rms=0.906 (35.678%) 023: dt: 0.2500, sse=1059137.5, rms=0.800 (11.643%) rms = 0.76, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=1038413.4, rms=0.764 (4.587%) rms = 0.73, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=1033734.3, rms=0.734 (3.873%) positioning took 0.7 minutes generating cortex label... 17 non-cortical segments detected only using segment with 12258 vertices erasing segment 0 (vno[0] = 35095) erasing segment 2 (vno[0] = 135044) erasing segment 3 (vno[0] = 146269) erasing segment 4 (vno[0] = 155811) erasing segment 5 (vno[0] = 157014) erasing segment 6 (vno[0] = 158429) erasing segment 7 (vno[0] = 162126) erasing segment 8 (vno[0] = 163359) erasing segment 9 (vno[0] = 164494) erasing segment 10 (vno[0] = 165603) erasing segment 11 (vno[0] = 167919) erasing segment 12 (vno[0] = 169073) erasing segment 13 (vno[0] = 170252) erasing segment 14 (vno[0] = 171382) erasing segment 15 (vno[0] = 171392) erasing segment 16 (vno[0] = 172355) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.area vertex spacing 0.70 +- 0.19 (0.02-->4.28) (max @ vno 52852 --> 219127) face area 0.20 +- 0.09 (0.00-->2.66) 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 109 points - only 0.00% unknown deleting segment 1 with 48 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 24 points - only 0.00% unknown deleting segment 8 with 62 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown deleting segment 10 with 21 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=75.0, 242 (242) missing vertices, mean dist 0.8 [1.8 (%0.0)->1.2 (%100.0))] %23 local maxima, %42 large gradients and %30 min vals, 93 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg43, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=18400968.0, rms=20.394 001: dt: 0.0500, sse=14426057.0, rms=17.915 (12.158%) 002: dt: 0.0500, sse=12315389.0, rms=16.446 (8.196%) 003: dt: 0.0500, sse=10944646.0, rms=15.418 (6.254%) 004: dt: 0.0500, sse=9950998.0, rms=14.627 (5.131%) 005: dt: 0.0500, sse=9177790.0, rms=13.980 (4.421%) 006: dt: 0.0500, sse=8544766.0, rms=13.427 (3.954%) 007: dt: 0.0500, sse=8008851.0, rms=12.941 (3.623%) 008: dt: 0.0500, sse=7543880.5, rms=12.503 (3.381%) 009: dt: 0.0500, sse=7133448.5, rms=12.104 (3.196%) 010: dt: 0.0500, sse=6766680.5, rms=11.735 (3.046%) positioning took 1.3 minutes mean border=69.6, 148 (96) missing vertices, mean dist 0.9 [0.1 (%0.0)->1.3 (%100.0))] %24 local maxima, %42 large gradients and %30 min vals, 172 gradients ignored tol=1.0e-04, sigma=2.0, host=blg43, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14132426.0, rms=17.713 011: dt: 0.0500, sse=13588254.0, rms=17.341 (2.098%) 012: dt: 0.0500, sse=13106820.0, rms=17.005 (1.936%) 013: dt: 0.0500, sse=12676995.0, rms=16.700 (1.797%) 014: dt: 0.0500, sse=12291157.0, rms=16.420 (1.672%) 015: dt: 0.0500, sse=11941301.0, rms=16.163 (1.568%) 016: dt: 0.0500, sse=11621901.0, rms=15.924 (1.478%) 017: dt: 0.0500, sse=11327692.0, rms=15.701 (1.402%) 018: dt: 0.0500, sse=11051696.0, rms=15.488 (1.353%) 019: dt: 0.0500, sse=10787110.0, rms=15.282 (1.333%) 020: dt: 0.0500, sse=10531870.0, rms=15.080 (1.320%) positioning took 1.3 minutes mean border=67.8, 144 (75) missing vertices, mean dist 0.9 [0.1 (%0.1)->1.2 (%99.9))] %24 local maxima, %42 large gradients and %29 min vals, 239 gradients ignored tol=1.0e-04, sigma=2.0, host=blg43, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11917195.0, rms=16.149 021: dt: 0.0500, sse=11608779.0, rms=15.918 (1.432%) 022: dt: 0.0500, sse=11318986.0, rms=15.697 (1.385%) 023: dt: 0.0500, sse=11045918.0, rms=15.487 (1.342%) 024: dt: 0.0500, sse=10787334.0, rms=15.284 (1.306%) 025: dt: 0.0500, sse=10541306.0, rms=15.089 (1.276%) 026: dt: 0.0500, sse=10304024.0, rms=14.899 (1.263%) 027: dt: 0.0500, sse=10073299.0, rms=14.711 (1.260%) 028: dt: 0.0500, sse=9848632.0, rms=14.526 (1.259%) 029: dt: 0.0500, sse=9628189.0, rms=14.342 (1.267%) 030: dt: 0.0500, sse=9410829.0, rms=14.158 (1.281%) positioning took 1.3 minutes mean border=66.9, 140 (60) missing vertices, mean dist 0.7 [0.1 (%2.1)->1.1 (%97.9))] %24 local maxima, %42 large gradients and %29 min vals, 223 gradients ignored tol=1.0e-04, sigma=2.0, host=blg43, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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=10206442.0, rms=14.815 031: dt: 0.5000, sse=8578324.0, rms=13.425 (9.379%) 032: dt: 0.5000, sse=7203578.0, rms=12.129 (9.652%) 033: dt: 0.5000, sse=5924020.0, rms=10.798 (10.977%) 034: dt: 0.5000, sse=4826590.5, rms=9.497 (12.043%) 035: dt: 0.5000, sse=3944419.8, rms=8.313 (12.466%) 036: dt: 0.5000, sse=3369503.8, rms=7.438 (10.534%) 037: dt: 0.5000, sse=3017389.8, rms=6.850 (7.903%) 038: dt: 0.5000, sse=2833725.5, rms=6.520 (4.813%) 039: dt: 0.5000, sse=2718506.8, rms=6.307 (3.269%) 040: dt: 0.5000, sse=2662408.8, rms=6.197 (1.744%) 041: dt: 0.5000, sse=2611103.8, rms=6.100 (1.563%) rms = 6.06, time step reduction 1 of 3 to 0.250... 042: dt: 0.5000, sse=2590682.2, rms=6.057 (0.714%) 043: dt: 0.2500, sse=2300624.0, rms=5.400 (10.834%) 044: dt: 0.2500, sse=2233216.0, rms=5.246 (2.867%) rms = 5.28, time step reduction 2 of 3 to 0.125... 045: dt: 0.1250, sse=2188018.2, rms=5.136 (2.093%) 046: dt: 0.1250, sse=2131394.0, rms=4.993 (2.771%) rms = 4.97, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=2124068.2, rms=4.974 (0.395%) positioning took 2.8 minutes mean border=63.6, 2964 (24) missing vertices, mean dist 0.3 [0.2 (%17.3)->0.5 (%82.7))] %42 local maxima, %25 large gradients and %27 min vals, 159 gradients ignored tol=1.0e-04, sigma=1.0, host=blg43, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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=3661995.5, rms=7.389 048: dt: 0.5000, sse=3455709.0, rms=7.022 (4.965%) 049: dt: 0.5000, sse=3029715.5, rms=6.263 (10.806%) 050: dt: 0.5000, sse=3010278.5, rms=6.212 (0.819%) 051: dt: 0.5000, sse=2638824.8, rms=5.454 (12.204%) rms = 5.45, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=2250059.5, rms=4.449 (18.422%) 053: dt: 0.2500, sse=2090558.1, rms=3.953 (11.150%) 054: dt: 0.2500, sse=2020657.9, rms=3.729 (5.675%) 055: dt: 0.2500, sse=1932527.1, rms=3.430 (8.012%) 056: dt: 0.2500, sse=1903757.8, rms=3.327 (2.997%) 057: dt: 0.2500, sse=1860067.8, rms=3.166 (4.855%) rms = 3.17, time step reduction 2 of 3 to 0.125... 058: dt: 0.1250, sse=1780798.1, rms=2.832 (10.548%) 059: dt: 0.1250, sse=1676163.6, rms=2.318 (18.123%) 060: dt: 0.1250, sse=1652669.8, rms=2.194 (5.384%) rms = 2.16, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1646581.6, rms=2.160 (1.522%) positioning took 2.9 minutes mean border=62.0, 3650 (18) missing vertices, mean dist 0.1 [0.2 (%21.3)->0.2 (%78.7))] %50 local maxima, %18 large gradients and %26 min vals, 140 gradients ignored tol=1.0e-04, sigma=0.5, host=blg43, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, 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=1961704.5, rms=3.374 rms = 4.67, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1822920.2, rms=2.817 (16.516%) 063: dt: 0.2500, sse=1788449.0, rms=2.655 (5.738%) rms = 2.76, time step reduction 2 of 3 to 0.125... 064: dt: 0.1250, sse=1767157.0, rms=2.553 (3.849%) 065: dt: 0.1250, sse=1741501.6, rms=2.429 (4.860%) 066: dt: 0.1250, sse=1726312.8, rms=2.355 (3.045%) rms = 2.31, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1717603.9, rms=2.314 (1.763%) positioning took 1.4 minutes mean border=61.3, 7680 (17) missing vertices, mean dist 0.0 [0.2 (%28.2)->0.1 (%71.8))] %52 local maxima, %15 large gradients and %24 min vals, 128 gradients ignored tol=1.0e-04, sigma=0.2, host=blg43, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1768534.8, rms=2.539 rms = 3.51, time step reduction 1 of 3 to 0.250... 068: dt: 0.2500, sse=1732972.6, rms=2.356 (7.226%) rms = 2.36, time step reduction 2 of 3 to 0.125... rms = 2.32, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1726981.9, rms=2.324 (1.341%) positioning took 0.6 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.area.pial vertex spacing 0.81 +- 0.36 (0.04-->6.82) (max @ vno 162365 --> 161115) face area 0.26 +- 0.21 (0.00-->5.79) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 219913 vertices processed 25000 of 219913 vertices processed 50000 of 219913 vertices processed 75000 of 219913 vertices processed 100000 of 219913 vertices processed 125000 of 219913 vertices processed 150000 of 219913 vertices processed 175000 of 219913 vertices processed 200000 of 219913 vertices processed 0 of 219913 vertices processed 25000 of 219913 vertices processed 50000 of 219913 vertices processed 75000 of 219913 vertices processed 100000 of 219913 vertices processed 125000 of 219913 vertices processed 150000 of 219913 vertices processed 175000 of 219913 vertices processed 200000 of 219913 vertices processed thickness calculation complete, 152:608 truncations. 36231 vertices at 0 distance 122381 vertices at 1 distance 133751 vertices at 2 distance 77842 vertices at 3 distance 31841 vertices at 4 distance 10876 vertices at 5 distance 3608 vertices at 6 distance 1244 vertices at 7 distance 415 vertices at 8 distance 163 vertices at 9 distance 113 vertices at 10 distance 76 vertices at 11 distance 46 vertices at 12 distance 48 vertices at 13 distance 36 vertices at 14 distance 24 vertices at 15 distance 18 vertices at 16 distance 19 vertices at 17 distance 12 vertices at 18 distance 12 vertices at 19 distance 12 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.thickness positioning took 19.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue May 25 23:13:03 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 sub-05 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Total face volume 255857 Total vertex volume 253692 (mask=0) #@# sub-05 lh 253692 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 lh Tue May 25 23:13:08 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/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 /opt/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... 111 labels changed using aseg relabeling using gibbs priors... 000: 13380 changed, 219913 examined... 001: 3359 changed, 51823 examined... 002: 1067 changed, 17183 examined... 003: 476 changed, 5907 examined... 004: 224 changed, 2688 examined... 005: 112 changed, 1304 examined... 006: 71 changed, 668 examined... 007: 43 changed, 393 examined... 008: 21 changed, 227 examined... 009: 8 changed, 121 examined... 010: 10 changed, 58 examined... 011: 3 changed, 48 examined... 012: 0 changed, 24 examined... 23 labels changed using aseg 000: 373 total segments, 284 labels (4015 vertices) changed 001: 104 total segments, 15 labels (31 vertices) changed 002: 89 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 56 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1534 vertices marked for relabeling... 1534 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# Cortical Parc 3 lh Tue May 25 23:13:28 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/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 /opt/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... 2649 labels changed using aseg relabeling using gibbs priors... 000: 2960 changed, 219913 examined... 001: 681 changed, 13344 examined... 002: 197 changed, 3884 examined... 003: 103 changed, 1170 examined... 004: 59 changed, 601 examined... 005: 57 changed, 346 examined... 006: 44 changed, 310 examined... 007: 23 changed, 236 examined... 008: 19 changed, 125 examined... 009: 15 changed, 107 examined... 010: 9 changed, 94 examined... 011: 7 changed, 62 examined... 012: 5 changed, 45 examined... 013: 3 changed, 29 examined... 014: 2 changed, 21 examined... 015: 3 changed, 15 examined... 016: 4 changed, 17 examined... 017: 3 changed, 20 examined... 018: 1 changed, 16 examined... 019: 1 changed, 7 examined... 020: 1 changed, 6 examined... 021: 1 changed, 7 examined... 022: 0 changed, 7 examined... 483 labels changed using aseg 000: 82 total segments, 49 labels (471 vertices) changed 001: 35 total segments, 2 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1064 vertices marked for relabeling... 1064 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# WM/GM Contrast lh Tue May 25 23:13:48 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts pctsurfcon --s sub-05 --lh-only Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts/pctsurfcon.log Tue May 25 23:13:48 UTC 2021 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux blg4313.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/tmp.pctsurfcon.202153/lh.wm.mgh --regheader sub-05 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 = 117545 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/tmp.pctsurfcon.202153/lh.wm.mgh Dim: 219913 1 1 mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/tmp.pctsurfcon.202153/lh.gm.mgh --projfrac 0.3 --regheader sub-05 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Done reading source surface Reading thickness /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 = 139042 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/tmp.pctsurfcon.202153/lh.gm.mgh Dim: 219913 1 1 mri_concat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/tmp.pctsurfcon.202153/lh.wm.mgh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/tmp.pctsurfcon.202153/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.w-g.pct.mgh mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.w-g.pct.mgh --annot sub-05 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.w-g.pct.mgh --annot sub-05 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/stats/lh.w-g.pct.stats --snr sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard UseRobust 0 Constructing seg from annotation Reading annotation /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.w-g.pct.mgh Vertex Area is 0.407965 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 Started at Tue May 25 21:12:52 UTC 2021 Ended at Tue May 25 23:14:07 UTC 2021 #@#%# recon-all-run-time-hours 2.021 recon-all -s sub-05 finished without error at Tue May 25 23:14:08 UTC 2021 New invocation of recon-all Wed May 26 00:55:00 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-05 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon subjid sub-05 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux blg4313.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638428 118564128 69133640 2008932 8940660 72913096 Swap: 0 0 0 ######################################## 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: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:00-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.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: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:55:01-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bpinsard Machine: blg4313.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Parcellation Stats lh Wed May 26 00:55:01 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 263179 Total vertex volume 260936 (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) = 1653081 mm^3 (det: 1.178470 ) lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 2259 987 2681 2.834 0.485 0.067 0.014 10 1.3 bankssts 1476 562 2105 2.756 0.853 0.090 0.026 18 1.7 caudalanteriorcingulate 6000 2503 7225 2.668 0.411 0.076 0.017 50 4.2 caudalmiddlefrontal 3513 1386 3748 2.313 0.460 0.098 0.026 42 3.9 cuneus 1048 453 2006 3.054 0.907 0.088 0.025 8 1.3 entorhinal 6979 2971 10836 2.889 0.660 0.095 0.031 103 10.0 fusiform 13388 5446 17178 2.737 0.484 0.085 0.021 144 11.9 inferiorparietal 9104 3775 14071 2.977 0.676 0.091 0.028 116 11.0 inferiortemporal 2615 1016 2747 2.210 0.965 0.097 0.032 37 3.4 isthmuscingulate 13318 5078 13550 2.286 0.572 0.095 0.026 162 14.3 lateraloccipital 5546 2340 8054 2.865 0.656 0.100 0.037 92 9.1 lateralorbitofrontal 7343 2878 8287 2.440 0.564 0.105 0.033 115 10.2 lingual 4167 1727 5723 2.637 0.719 0.090 0.025 62 4.3 medialorbitofrontal 7765 3160 11393 2.772 0.666 0.092 0.026 104 8.2 middletemporal 1281 534 2035 3.323 0.783 0.078 0.020 7 1.1 parahippocampal 3063 1283 3992 2.705 0.605 0.080 0.018 21 2.5 paracentral 3229 1379 4378 2.714 0.592 0.084 0.021 31 2.8 parsopercularis 1425 588 2225 2.740 0.654 0.104 0.030 22 1.8 parsorbitalis 2982 1267 3736 2.550 0.622 0.081 0.019 30 2.4 parstriangularis 4072 1510 3572 2.400 0.451 0.090 0.034 54 6.0 pericalcarine 9227 3546 9362 2.285 0.618 0.078 0.021 85 8.3 postcentral 2115 882 2605 2.406 0.855 0.102 0.025 29 2.2 posteriorcingulate 13028 4895 15157 2.801 0.515 0.076 0.028 121 17.2 precentral 9832 4132 11817 2.558 0.500 0.089 0.023 117 9.3 precuneus 1312 545 1955 2.848 0.759 0.097 0.027 23 1.6 rostralanteriorcingulate 14530 6024 17081 2.386 0.531 0.096 0.026 195 16.1 rostralmiddlefrontal 16539 6891 22550 2.730 0.616 0.085 0.025 169 17.6 superiorfrontal 14291 5711 15037 2.291 0.461 0.082 0.020 157 12.0 superiorparietal 8017 3402 10766 2.674 0.683 0.073 0.019 66 7.0 superiortemporal 8684 3607 10778 2.667 0.476 0.090 0.022 91 8.0 supramarginal 1074 418 1500 2.544 0.517 0.121 0.044 24 2.2 frontalpole 1713 724 3713 3.455 0.745 0.107 0.041 28 3.4 temporalpole 1154 449 1379 2.823 0.408 0.089 0.023 13 1.1 transversetemporal 5155 2269 7637 3.130 0.958 0.109 0.050 78 11.7 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 sub-05 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 263179 Total vertex volume 260936 (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) = 1653081 mm^3 (det: 1.178470 ) lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 2259 888 2681 2.834 0.485 0.074 0.020 17 1.9 bankssts 1476 831 2105 2.756 0.853 0.108 0.030 48 1.7 caudalanteriorcingulate 6000 2792 7225 2.668 0.411 0.074 0.016 60 4.0 caudalmiddlefrontal 3513 1731 3748 2.313 0.460 0.086 0.020 27 2.8 cuneus 1048 808 2006 3.054 0.907 0.116 0.022 9 1.2 entorhinal 6979 4128 10836 2.889 0.660 0.099 0.024 82 7.1 fusiform 13388 6756 17178 2.737 0.484 0.084 0.020 152 11.5 inferiorparietal 9104 5136 14071 2.977 0.676 0.097 0.074 5059 9.8 inferiortemporal 2615 1287 2747 2.210 0.965 0.096 0.029 39 2.8 isthmuscingulate 13318 6291 13550 2.286 0.572 0.078 0.020 161 10.4 lateraloccipital 5546 2997 8054 2.865 0.656 0.100 0.029 76 7.2 lateralorbitofrontal 7343 3685 8287 2.440 0.564 0.094 0.028 113 8.1 lingual 4167 2369 5723 2.637 0.719 0.094 0.023 45 3.5 medialorbitofrontal 7765 4602 11393 2.772 0.666 0.098 0.022 69 7.4 middletemporal 1281 688 2035 3.323 0.783 0.088 0.021 12 1.1 parahippocampal 3063 1558 3992 2.705 0.605 0.082 0.018 23 2.3 paracentral 3229 1690 4378 2.714 0.592 0.086 0.019 28 2.6 parsopercularis 1425 921 2225 2.740 0.654 0.109 0.024 13 1.6 parsorbitalis 2982 1581 3736 2.550 0.622 0.092 0.019 28 2.4 parstriangularis 4072 1409 3572 2.400 0.451 0.073 0.022 46 3.5 pericalcarine 9227 4438 9362 2.285 0.618 0.076 0.016 84 6.0 postcentral 2115 1130 2605 2.406 0.855 0.104 0.031 35 2.5 posteriorcingulate 13028 5674 15157 2.801 0.515 0.067 0.017 97 9.5 precentral 9832 4760 11817 2.558 0.500 0.089 0.024 124 9.1 precuneus 1312 797 1955 2.848 0.759 0.103 0.026 18 1.2 rostralanteriorcingulate 14530 7664 17081 2.386 0.531 0.099 0.024 156 15.5 rostralmiddlefrontal 16539 8767 22550 2.730 0.616 0.091 0.023 559 15.0 superiorfrontal 14291 6980 15037 2.291 0.461 0.084 0.021 143 12.9 superiorparietal 8017 4320 10766 2.674 0.683 0.089 0.022 68 7.4 superiortemporal 8684 4229 10778 2.667 0.476 0.085 0.021 115 7.9 supramarginal 1074 691 1500 2.544 0.517 0.135 0.032 14 1.6 frontalpole 1713 1320 3713 3.455 0.745 0.123 0.027 20 1.9 temporalpole 1154 528 1379 2.823 0.408 0.076 0.019 25 0.9 transversetemporal 5155 2318 7637 3.130 0.958 0.104 0.043 308 11.4 insula #----------------------------------------- #@# Parcellation Stats 2 lh Wed May 26 00:57:23 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 263179 Total vertex volume 260936 (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) = 1653081 mm^3 (det: 1.178470 ) lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 2590 1055 2520 2.115 0.503 0.100 0.031 40 3.5 G&S_frontomargin 2895 1188 3312 2.417 0.549 0.087 0.019 28 2.0 G&S_occipital_inf 3127 1130 3495 2.532 0.529 0.080 0.026 31 4.2 G&S_paracentral 2242 921 3474 3.079 0.504 0.098 0.026 25 2.6 G&S_subcentral 1692 654 2116 2.384 0.608 0.112 0.042 33 3.1 G&S_transv_frontopol 3158 1305 4339 2.786 0.622 0.089 0.024 39 3.3 G&S_cingul-Ant 1775 731 2389 2.917 0.572 0.083 0.024 16 1.8 G&S_cingul-Mid-Ant 1818 765 2278 2.730 0.571 0.080 0.019 14 1.4 G&S_cingul-Mid-Post 868 366 1665 3.089 0.731 0.128 0.045 18 1.8 G_cingul-Post-dorsal 502 180 599 2.467 0.924 0.117 0.049 11 0.9 G_cingul-Post-ventral 3376 1250 3842 2.288 0.496 0.108 0.036 60 5.2 G_cuneus 1791 747 3445 3.158 0.439 0.110 0.030 31 2.3 G_front_inf-Opercular 665 265 1277 3.259 0.396 0.117 0.038 14 1.0 G_front_inf-Orbital 1645 694 2396 2.528 0.617 0.095 0.023 23 1.7 G_front_inf-Triangul 8144 3368 12040 2.641 0.519 0.102 0.028 130 9.5 G_front_middle 11077 4606 18302 2.928 0.640 0.100 0.032 157 15.5 G_front_sup 806 352 1714 3.875 0.732 0.127 0.053 15 2.1 G_Ins_lg&S_cent_ins 1213 522 2378 3.503 0.830 0.149 0.085 26 5.4 G_insular_short 4386 1741 6600 2.718 0.587 0.114 0.032 87 5.9 G_occipital_middle 2197 866 2604 2.332 0.479 0.093 0.021 27 1.9 G_occipital_sup 2578 1068 4988 3.185 0.558 0.114 0.034 50 3.7 G_oc-temp_lat-fusifor 4853 1804 6189 2.520 0.623 0.115 0.040 100 8.2 G_oc-temp_med-Lingual 2073 895 4290 3.380 0.808 0.099 0.032 20 3.1 G_oc-temp_med-Parahip 3640 1525 6331 2.914 0.635 0.113 0.046 90 7.3 G_orbital 5191 2001 7712 2.816 0.522 0.100 0.027 80 5.8 G_pariet_inf-Angular 4194 1717 6270 2.782 0.497 0.100 0.025 59 4.6 G_pariet_inf-Supramar 6383 2429 7409 2.358 0.531 0.088 0.026 93 6.8 G_parietal_sup 3392 1130 3178 2.190 0.422 0.080 0.023 40 3.3 G_postcentral 5012 1648 6797 3.072 0.475 0.086 0.040 65 9.8 G_precentral 4395 1831 7032 2.762 0.512 0.112 0.032 93 6.2 G_precuneus 1473 585 2583 2.932 0.656 0.111 0.036 38 2.3 G_rectus 960 408 1095 2.482 1.165 0.092 0.050 12 1.4 G_subcallosal 633 254 1030 3.130 0.357 0.106 0.030 10 0.7 G_temp_sup-G_T_transv 2873 1177 4549 2.729 0.677 0.093 0.028 42 3.4 G_temp_sup-Lateral 1534 661 2379 3.205 0.898 0.074 0.027 11 1.8 G_temp_sup-Plan_polar 1318 574 1630 2.426 0.541 0.067 0.013 7 0.7 G_temp_sup-Plan_tempo 5168 2093 9932 3.218 0.646 0.106 0.038 95 8.4 G_temporal_inf 4275 1678 7337 2.950 0.624 0.106 0.035 79 6.1 G_temporal_middle 474 195 529 2.740 0.558 0.071 0.016 2 0.3 Lat_Fis-ant-Horizont 580 247 476 2.392 0.388 0.056 0.009 2 0.2 Lat_Fis-ant-Vertical 2276 938 2158 2.647 0.408 0.075 0.019 13 1.8 Lat_Fis-post 4347 1397 3488 2.070 0.578 0.087 0.029 52 5.5 Pole_occipital 3171 1333 6467 3.121 0.732 0.106 0.046 74 7.3 Pole_temporal 4221 1698 3695 2.412 0.500 0.083 0.027 41 4.7 S_calcarine 5149 2144 4249 2.232 0.546 0.067 0.020 30 4.3 S_central 1499 657 1337 2.229 0.388 0.060 0.009 4 0.6 S_cingul-Marginalis 733 320 972 3.144 0.578 0.072 0.018 3 0.7 S_circular_insula_ant 1927 848 2075 2.736 0.704 0.069 0.021 22 1.9 S_circular_insula_inf 2374 1047 2480 2.839 0.571 0.074 0.020 10 2.1 S_circular_insula_sup 1961 866 2034 2.518 0.651 0.067 0.012 7 1.0 S_collat_transv_ant 815 370 610 1.979 0.322 0.082 0.015 4 0.6 S_collat_transv_post 4423 1872 4167 2.273 0.382 0.071 0.013 28 2.5 S_front_inf 1988 855 1708 2.212 0.436 0.084 0.020 14 1.7 S_front_middle 4125 1765 4132 2.436 0.444 0.062 0.013 17 2.1 S_front_sup 541 231 522 2.511 0.409 0.077 0.017 2 0.4 S_interm_prim-Jensen 5811 2428 5108 2.268 0.362 0.070 0.013 31 3.2 S_intrapariet&P_trans 1012 423 768 2.142 0.426 0.085 0.021 6 0.8 S_oc_middle&Lunatus 2131 905 1873 2.325 0.322 0.077 0.016 12 1.3 S_oc_sup&transversal 1241 531 1285 2.688 0.349 0.080 0.019 6 0.9 S_occipital_ant 1299 554 1285 2.715 0.442 0.063 0.012 4 0.6 S_oc-temp_lat 3316 1417 3305 2.605 0.496 0.080 0.018 18 2.5 S_oc-temp_med&Lingual 562 232 447 2.043 0.324 0.073 0.012 2 0.3 S_orbital_lateral 921 405 901 2.345 0.777 0.078 0.014 5 0.6 S_orbital_med-olfact 2114 866 2469 2.603 0.662 0.094 0.027 19 2.4 S_orbital-H_Shaped 4494 1868 4264 2.394 0.376 0.075 0.017 28 3.3 S_parieto_occipital 1862 711 759 1.428 0.505 0.087 0.018 21 1.1 S_pericallosal 3646 1554 3090 2.198 0.353 0.068 0.013 19 1.9 S_postcentral 3017 1268 3155 2.643 0.411 0.071 0.014 18 1.6 S_precentral-inf-part 2450 1079 2276 2.496 0.346 0.055 0.009 5 0.9 S_precentral-sup-part 1250 511 1061 2.274 0.421 0.064 0.009 5 0.5 S_suborbital 2241 927 2072 2.534 0.410 0.085 0.021 17 2.0 S_subparietal 2865 1217 2588 2.455 0.566 0.070 0.014 13 1.5 S_temporal_inf 10066 4287 11165 2.674 0.537 0.069 0.015 58 6.5 S_temporal_sup 417 182 450 2.717 0.387 0.061 0.010 1 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 lh Wed May 26 00:58:28 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 263179 Total vertex volume 260936 (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) = 1653081 mm^3 (det: 1.178470 ) lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 2130 847 2697 2.739 0.762 0.087 0.024 22 2.1 caudalanteriorcingulate 6419 2679 7910 2.693 0.422 0.076 0.017 54 4.4 caudalmiddlefrontal 5055 2022 5464 2.350 0.450 0.091 0.023 54 4.9 cuneus 921 409 1846 3.098 0.907 0.088 0.025 7 1.1 entorhinal 6182 2662 9610 2.900 0.645 0.092 0.025 72 6.4 fusiform 13437 5462 16758 2.700 0.488 0.086 0.022 147 12.2 inferiorparietal 9231 3802 14691 2.994 0.676 0.095 0.034 144 14.3 inferiortemporal 2604 1011 2770 2.230 0.966 0.097 0.032 38 3.4 isthmuscingulate 13242 5057 13482 2.284 0.574 0.095 0.025 158 14.1 lateraloccipital 6511 2727 9393 2.781 0.694 0.107 0.042 122 12.1 lateralorbitofrontal 7643 2977 8516 2.422 0.559 0.104 0.032 118 10.5 lingual 3789 1531 4992 2.570 0.831 0.090 0.029 58 4.3 medialorbitofrontal 10644 4369 14681 2.785 0.637 0.087 0.023 122 10.2 middletemporal 1330 559 2116 3.313 0.772 0.077 0.020 7 1.1 parahippocampal 3673 1542 4795 2.722 0.590 0.077 0.017 23 2.8 paracentral 2914 1230 4039 2.792 0.553 0.088 0.023 30 2.7 parsopercularis 1427 599 1971 2.810 0.622 0.089 0.023 16 1.4 parsorbitalis 3803 1636 4502 2.432 0.602 0.079 0.018 38 2.9 parstriangularis 3836 1423 3403 2.429 0.442 0.089 0.035 51 5.8 pericalcarine 10290 4000 10400 2.289 0.609 0.079 0.020 93 9.1 postcentral 2389 989 2821 2.424 0.832 0.099 0.024 30 2.4 posteriorcingulate 12803 4806 14853 2.807 0.510 0.077 0.029 119 17.2 precentral 9545 4002 11657 2.546 0.510 0.091 0.023 119 9.4 precuneus 1846 765 2727 2.803 0.735 0.093 0.026 29 2.0 rostralanteriorcingulate 10454 4343 12553 2.400 0.516 0.093 0.025 132 10.7 rostralmiddlefrontal 19091 7914 25782 2.663 0.634 0.091 0.027 228 22.5 superiorfrontal 11882 4716 12335 2.289 0.465 0.081 0.021 132 10.3 superiorparietal 11061 4725 16130 2.799 0.732 0.079 0.023 105 11.4 superiortemporal 7889 3284 10042 2.685 0.465 0.090 0.021 81 7.2 supramarginal 1135 441 1358 2.809 0.421 0.089 0.023 13 1.1 transversetemporal 4055 1807 6642 3.326 0.830 0.109 0.047 61 9.3 insula /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed May 26 00:59:43 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1152 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 5281 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1153 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9062 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 818 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4895 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1417 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 7400 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 2009 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 7793 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1340 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 5410 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 5780 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 19369 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1129 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 5310 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 2039 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 5461 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-05 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 5021 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 9662 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-05 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 8790 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 16904 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-05 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1786 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 3804 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-05 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 541 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1831 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-05 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 643 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1842 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1381 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1665 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2615 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 1114 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 3433 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 578 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 2127 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 2564 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 9599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 322 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2234 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 741 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1892 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 3539 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 6944 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 4009 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 7343 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 515 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 1028 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 164 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 634 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 219913 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 715 mri_label2label: Done mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 /opt/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label cmdline mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-05 hemi lh SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 152607 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label/lh.BA_exvivo.annot mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 /opt/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/label cmdline mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-05 hemi lh SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 179765 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 263179 Total vertex volume 260936 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 1653081 mm^3 (det: 1.178470 ) lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 1844 582 1826 2.300 0.458 0.085 0.026 25 1.9 BA1_exvivo 4673 1894 4456 2.283 0.394 0.073 0.015 37 2.9 BA2_exvivo 1513 666 1135 2.080 0.351 0.076 0.018 7 1.0 BA3a_exvivo 3596 1416 3477 2.074 0.590 0.078 0.020 31 3.3 BA3b_exvivo 2950 1042 4006 3.006 0.492 0.080 0.032 33 4.8 BA4a_exvivo 2529 935 2579 2.759 0.480 0.072 0.036 28 4.2 BA4p_exvivo 15761 6376 21804 2.830 0.575 0.085 0.027 166 19.2 BA6_exvivo 3240 1360 4497 2.855 0.533 0.085 0.020 30 2.6 BA44_exvivo 4732 2002 5729 2.399 0.528 0.082 0.019 50 3.7 BA45_exvivo 6531 2367 5717 2.321 0.505 0.089 0.032 78 9.1 V1_exvivo 14022 5288 14515 2.263 0.554 0.101 0.030 204 17.7 V2_exvivo 3673 1508 4971 2.735 0.480 0.095 0.023 44 3.5 MT_exvivo 898 387 1825 3.181 0.953 0.083 0.023 6 1.0 perirhinal_exvivo 1344 580 2646 3.318 0.696 0.099 0.034 16 1.9 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 sub-05 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 263179 Total vertex volume 260936 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 1653081 mm^3 (det: 1.178470 ) lhCtxGM: 256160.873 505832.000 diff=-249671.1 pctdiff=-97.467 rhCtxGM: 254732.889 500365.000 diff=-245632.1 pctdiff=-96.427 lhCtxWM: 178195.530 407102.000 diff=-228906.5 pctdiff=-128.458 rhCtxWM: 179705.335 409193.000 diff=-229487.7 pctdiff=-127.702 SubCortGMVol 115338.000 SupraTentVol 999716.626 (1967040.000) diff=-967323.374 pctdiff=-96.760 SupraTentVolNotVent 970539.626 (1937863.000) diff=-967323.374 pctdiff=-99.669 BrainSegVol 2258964.000 (2252858.000) diff=6106.000 pctdiff=0.270 BrainSegVolNotVent 2221705.000 (1267774.626) diff=953930.374 pctdiff=42.937 BrainSegVolNotVent 2221705.000 CerebellumVol 283609.000 VentChorVol 29177.000 3rd4th5thCSF 8082.000 CSFVol 1976.000, OptChiasmVol 233.000 MaskVol 2805483.000 1179 352 1202 2.353 0.397 0.089 0.025 15 1.1 BA1_exvivo 1919 759 1818 2.229 0.301 0.061 0.012 13 1.0 BA2_exvivo 1275 570 884 2.021 0.301 0.079 0.020 5 1.0 BA3a_exvivo 2319 917 1773 1.844 0.395 0.064 0.015 12 1.6 BA3b_exvivo 3098 1069 3780 2.959 0.515 0.069 0.026 23 4.0 BA4a_exvivo 1957 743 1989 2.731 0.439 0.070 0.031 21 2.7 BA4p_exvivo 8512 3344 11358 2.828 0.557 0.084 0.030 90 11.6 BA6_exvivo 1871 781 2801 2.888 0.540 0.092 0.021 21 1.7 BA44_exvivo 1825 778 2273 2.319 0.535 0.086 0.021 22 1.7 BA45_exvivo 6834 2473 6039 2.316 0.513 0.090 0.032 82 9.8 V1_exvivo 7185 2573 6831 2.172 0.548 0.100 0.031 114 9.2 V2_exvivo 1023 446 1192 2.531 0.417 0.095 0.021 9 1.0 MT_exvivo 462 205 810 2.924 0.808 0.067 0.013 2 0.3 perirhinal_exvivo 689 304 1215 3.366 0.799 0.101 0.030 7 0.8 entorhinal_exvivo Started at Wed May 26 00:54:57 UTC 2021 Ended at Wed May 26 01:06:06 UTC 2021 #@#%# recon-all-run-time-hours 0.186 recon-all -s sub-05 finished without error at Wed May 26 01:06:06 UTC 2021