Sat May 22 04:55:05 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-01 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-01 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 blg5521.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 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 56269956 114278936 2261496 26089368 133750840 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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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: 2021/05/22-04:55:06-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: blg5521.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 Sat May 22 04:55:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 3 found - 3 modified | TOTAL: 5 pass 2 (yz-): 0 found - 3 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 9 (out of 509067: 0.001768) 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 40: 1429 vertices, 1563 faces slice 50: 8802 vertices, 9141 faces slice 60: 20137 vertices, 20539 faces slice 70: 31476 vertices, 31953 faces slice 80: 45168 vertices, 45657 faces slice 90: 58474 vertices, 58942 faces slice 100: 72025 vertices, 72533 faces slice 110: 86022 vertices, 86498 faces slice 120: 100991 vertices, 101537 faces slice 130: 116624 vertices, 117203 faces slice 140: 132503 vertices, 133037 faces slice 150: 147856 vertices, 148424 faces slice 160: 163047 vertices, 163585 faces slice 170: 177001 vertices, 177510 faces slice 180: 189837 vertices, 190306 faces slice 190: 200971 vertices, 201379 faces slice 200: 210646 vertices, 211024 faces slice 210: 219981 vertices, 220331 faces slice 220: 228114 vertices, 228443 faces slice 230: 234941 vertices, 235193 faces slice 240: 239554 vertices, 239712 faces slice 250: 240154 vertices, 240204 faces slice 260: 240154 vertices, 240204 faces slice 270: 240154 vertices, 240204 faces slice 280: 240154 vertices, 240204 faces slice 290: 240154 vertices, 240204 faces slice 300: 240154 vertices, 240204 faces slice 310: 240154 vertices, 240204 faces slice 320: 240154 vertices, 240204 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... 240142 voxel in cpt #1: X=-52 [v=240142,e=720582,f=480388] located at (-27.284943, -22.271181, 28.990383) 12 voxel in cpt #2: X=2 [v=12,e=30,f=20] located at (-1.599998, 6.799995, 26.399996) For the whole surface: X=-50 [v=240154,e=720612,f=480408] 2 components have been found keeping component #1 with 240142 vertices done #-------------------------------------------- #@# Smooth1 lh Sat May 22 04:55:14 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 Sat May 22 04:55:22 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 = 47.9 mm, total surface area = 84713 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.6 minutes step 000: RMS=0.140 (target=0.015) step 005: RMS=0.107 (target=0.015) step 010: RMS=0.080 (target=0.015) step 015: RMS=0.067 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) step 065: RMS=0.032 (target=0.015) step 070: RMS=0.031 (target=0.015) step 075: RMS=0.031 (target=0.015) step 080: RMS=0.030 (target=0.015) step 085: RMS=0.030 (target=0.015) step 090: RMS=0.030 (target=0.015) step 095: RMS=0.030 (target=0.015) step 100: RMS=0.029 (target=0.015) step 105: RMS=0.029 (target=0.015) step 110: RMS=0.029 (target=0.015) step 115: RMS=0.029 (target=0.015) step 120: RMS=0.029 (target=0.015) step 125: RMS=0.029 (target=0.015) step 130: RMS=0.029 (target=0.015) step 135: RMS=0.029 (target=0.015) step 140: RMS=0.029 (target=0.015) step 145: RMS=0.029 (target=0.015) step 150: RMS=0.029 (target=0.015) step 155: RMS=0.029 (target=0.015) step 160: RMS=0.029 (target=0.015) step 165: RMS=0.029 (target=0.015) step 170: RMS=0.029 (target=0.015) step 175: RMS=0.029 (target=0.015) step 180: RMS=0.029 (target=0.015) step 185: RMS=0.029 (target=0.015) step 190: RMS=0.029 (target=0.015) step 195: RMS=0.029 (target=0.015) step 200: RMS=0.029 (target=0.015) step 205: RMS=0.029 (target=0.015) step 210: RMS=0.029 (target=0.015) step 215: RMS=0.029 (target=0.015) step 220: RMS=0.029 (target=0.015) step 225: RMS=0.029 (target=0.015) step 230: RMS=0.029 (target=0.015) step 235: RMS=0.029 (target=0.015) step 240: RMS=0.029 (target=0.015) step 245: RMS=0.029 (target=0.015) step 250: RMS=0.029 (target=0.015) step 255: RMS=0.030 (target=0.015) step 260: RMS=0.030 (target=0.015) step 265: RMS=0.031 (target=0.015) step 270: RMS=0.031 (target=0.015) step 275: RMS=0.031 (target=0.015) step 280: RMS=0.030 (target=0.015) step 285: RMS=0.031 (target=0.015) step 290: RMS=0.030 (target=0.015) step 295: RMS=0.031 (target=0.015) step 300: RMS=0.030 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 457.346499 mris_inflate stimesec 1.911642 mris_inflate ru_maxrss 382992 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 935256 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 16896 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 66278 mris_inflate ru_nivcsw 562 #-------------------------------------------- #@# QSphere lh Sat May 22 04:56:57 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 0.74 +- 0.42 (0.00-->4.81) (max @ vno 80418 --> 81644) face area 0.01 +- 0.02 (-0.04-->0.36) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.288... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.643, avgs=0 005/300: dt: 0.9000, rms radial error=175.382, avgs=0 010/300: dt: 0.9000, rms radial error=174.824, avgs=0 015/300: dt: 0.9000, rms radial error=174.090, avgs=0 020/300: dt: 0.9000, rms radial error=173.254, avgs=0 025/300: dt: 0.9000, rms radial error=172.359, avgs=0 030/300: dt: 0.9000, rms radial error=171.432, avgs=0 035/300: dt: 0.9000, rms radial error=170.488, avgs=0 040/300: dt: 0.9000, rms radial error=169.536, avgs=0 045/300: dt: 0.9000, rms radial error=168.581, avgs=0 050/300: dt: 0.9000, rms radial error=167.628, avgs=0 055/300: dt: 0.9000, rms radial error=166.677, avgs=0 060/300: dt: 0.9000, rms radial error=165.730, avgs=0 065/300: dt: 0.9000, rms radial error=164.788, avgs=0 070/300: dt: 0.9000, rms radial error=163.852, avgs=0 075/300: dt: 0.9000, rms radial error=162.921, avgs=0 080/300: dt: 0.9000, rms radial error=161.996, avgs=0 085/300: dt: 0.9000, rms radial error=161.076, avgs=0 090/300: dt: 0.9000, rms radial error=160.161, avgs=0 095/300: dt: 0.9000, rms radial error=159.252, avgs=0 100/300: dt: 0.9000, rms radial error=158.347, avgs=0 105/300: dt: 0.9000, rms radial error=157.448, avgs=0 110/300: dt: 0.9000, rms radial error=156.558, avgs=0 115/300: dt: 0.9000, rms radial error=155.672, avgs=0 120/300: dt: 0.9000, rms radial error=154.791, avgs=0 125/300: dt: 0.9000, rms radial error=153.916, avgs=0 130/300: dt: 0.9000, rms radial error=153.045, avgs=0 135/300: dt: 0.9000, rms radial error=152.179, avgs=0 140/300: dt: 0.9000, rms radial error=151.318, avgs=0 145/300: dt: 0.9000, rms radial error=150.462, avgs=0 150/300: dt: 0.9000, rms radial error=149.610, avgs=0 155/300: dt: 0.9000, rms radial error=148.764, avgs=0 160/300: dt: 0.9000, rms radial error=147.922, avgs=0 165/300: dt: 0.9000, rms radial error=147.085, avgs=0 170/300: dt: 0.9000, rms radial error=146.253, avgs=0 175/300: dt: 0.9000, rms radial error=145.425, avgs=0 180/300: dt: 0.9000, rms radial error=144.602, avgs=0 185/300: dt: 0.9000, rms radial error=143.784, avgs=0 190/300: dt: 0.9000, rms radial error=142.970, avgs=0 195/300: dt: 0.9000, rms radial error=142.161, avgs=0 200/300: dt: 0.9000, rms radial error=141.357, avgs=0 205/300: dt: 0.9000, rms radial error=140.557, avgs=0 210/300: dt: 0.9000, rms radial error=139.762, avgs=0 215/300: dt: 0.9000, rms radial error=138.971, avgs=0 220/300: dt: 0.9000, rms radial error=138.185, avgs=0 225/300: dt: 0.9000, rms radial error=137.403, avgs=0 230/300: dt: 0.9000, rms radial error=136.626, avgs=0 235/300: dt: 0.9000, rms radial error=135.853, avgs=0 240/300: dt: 0.9000, rms radial error=135.084, avgs=0 245/300: dt: 0.9000, rms radial error=134.320, avgs=0 250/300: dt: 0.9000, rms radial error=133.560, avgs=0 255/300: dt: 0.9000, rms radial error=132.805, avgs=0 260/300: dt: 0.9000, rms radial error=132.054, avgs=0 265/300: dt: 0.9000, rms radial error=131.307, avgs=0 270/300: dt: 0.9000, rms radial error=130.564, avgs=0 275/300: dt: 0.9000, rms radial error=129.825, avgs=0 280/300: dt: 0.9000, rms radial error=129.091, avgs=0 285/300: dt: 0.9000, rms radial error=128.361, avgs=0 290/300: dt: 0.9000, rms radial error=127.634, avgs=0 295/300: dt: 0.9000, rms radial error=126.912, avgs=0 300/300: dt: 0.9000, rms radial error=126.195, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 30077.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 5748.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 724.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00350 epoch 4 (K=640.0), pass 1, starting sse = 52.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/14 = 0.00731 final distance error %26.25 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 561.275829 mris_sphere stimesec 1.693359 mris_sphere ru_maxrss 383332 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 594616 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 16896 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 87703 mris_sphere ru_nivcsw 611 FSRUNTIME@ mris_sphere 0.0383 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sat May 22 04:59:15 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Sat May 22 04:59:15 UTC 2021 mris_fix_topology -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-01 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=-52 (nv=240142, nf=480388, ne=720582, g=27) 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... 4127 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 11 -merging segment 19 into 17 53 defects to be corrected 0 vertices coincident reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4058 (-4.7029) -vertex loglikelihood: -5.8140 (-2.9070) -normal dot loglikelihood: -3.5913 (-3.5913) -quad curv loglikelihood: -6.5137 (-3.2569) Total Loglikelihood : -25.3248 CORRECTING DEFECT 0 (vertices=33, convex hull=60, v0=5956) After retessellation of defect 0 (v0=5956), euler #=-52 (237598,711815,474165) : difference with theory (-50) = 2 CORRECTING DEFECT 1 (vertices=105, convex hull=145, v0=8225) After retessellation of defect 1 (v0=8225), euler #=-51 (237611,711917,474255) : difference with theory (-49) = 2 CORRECTING DEFECT 2 (vertices=63, convex hull=86, v0=10309) After retessellation of defect 2 (v0=10309), euler #=-50 (237626,712002,474326) : difference with theory (-48) = 2 CORRECTING DEFECT 3 (vertices=24, convex hull=23, v0=10874) After retessellation of defect 3 (v0=10874), euler #=-49 (237629,712017,474339) : difference with theory (-47) = 2 CORRECTING DEFECT 4 (vertices=27, convex hull=49, v0=12982) After retessellation of defect 4 (v0=12982), euler #=-48 (237633,712047,474366) : difference with theory (-46) = 2 CORRECTING DEFECT 5 (vertices=254, convex hull=42, v0=14823) After retessellation of defect 5 (v0=14823), euler #=-47 (237638,712077,474392) : difference with theory (-45) = 2 CORRECTING DEFECT 6 (vertices=29, convex hull=57, v0=29849) After retessellation of defect 6 (v0=29849), euler #=-46 (237644,712111,474421) : difference with theory (-44) = 2 CORRECTING DEFECT 7 (vertices=18, convex hull=36, v0=39189) After retessellation of defect 7 (v0=39189), euler #=-45 (237647,712131,474439) : difference with theory (-43) = 2 CORRECTING DEFECT 8 (vertices=6, convex hull=27, v0=45933) After retessellation of defect 8 (v0=45933), euler #=-44 (237649,712145,474452) : difference with theory (-42) = 2 CORRECTING DEFECT 9 (vertices=18, convex hull=75, v0=61973) After retessellation of defect 9 (v0=61973), euler #=-43 (237654,712187,474490) : difference with theory (-41) = 2 CORRECTING DEFECT 10 (vertices=6, convex hull=17, v0=69250) After retessellation of defect 10 (v0=69250), euler #=-42 (237654,712193,474497) : difference with theory (-40) = 2 CORRECTING DEFECT 11 (vertices=48, convex hull=67, v0=73032) After retessellation of defect 11 (v0=73032), euler #=-40 (237663,712253,474550) : difference with theory (-39) = 1 CORRECTING DEFECT 12 (vertices=100, convex hull=82, v0=75868) After retessellation of defect 12 (v0=75868), euler #=-39 (237673,712317,474605) : difference with theory (-38) = 1 CORRECTING DEFECT 13 (vertices=40, convex hull=50, v0=91035) After retessellation of defect 13 (v0=91035), euler #=-38 (237682,712364,474644) : difference with theory (-37) = 1 CORRECTING DEFECT 14 (vertices=38, convex hull=61, v0=101044) After retessellation of defect 14 (v0=101044), euler #=-37 (237691,712415,474687) : difference with theory (-36) = 1 CORRECTING DEFECT 15 (vertices=47, convex hull=38, v0=101913) After retessellation of defect 15 (v0=101913), euler #=-36 (237696,712440,474708) : difference with theory (-35) = 1 CORRECTING DEFECT 16 (vertices=63, convex hull=73, v0=107331) After retessellation of defect 16 (v0=107331), euler #=-34 (237705,712505,474766) : difference with theory (-34) = 0 CORRECTING DEFECT 17 (vertices=24, convex hull=73, v0=108916) After retessellation of defect 17 (v0=108916), euler #=-33 (237711,712551,474807) : difference with theory (-33) = 0 CORRECTING DEFECT 18 (vertices=36, convex hull=72, v0=110495) After retessellation of defect 18 (v0=110495), euler #=-32 (237722,712613,474859) : difference with theory (-32) = 0 CORRECTING DEFECT 19 (vertices=26, convex hull=47, v0=115021) After retessellation of defect 19 (v0=115021), euler #=-31 (237728,712646,474887) : difference with theory (-31) = 0 CORRECTING DEFECT 20 (vertices=51, convex hull=72, v0=123761) After retessellation of defect 20 (v0=123761), euler #=-30 (237737,712705,474938) : difference with theory (-30) = 0 CORRECTING DEFECT 21 (vertices=53, convex hull=70, v0=125287) After retessellation of defect 21 (v0=125287), euler #=-29 (237751,712773,474993) : difference with theory (-29) = 0 CORRECTING DEFECT 22 (vertices=140, convex hull=56, v0=127739) After retessellation of defect 22 (v0=127739), euler #=-28 (237758,712816,475030) : difference with theory (-28) = 0 CORRECTING DEFECT 23 (vertices=10, convex hull=33, v0=128907) After retessellation of defect 23 (v0=128907), euler #=-27 (237760,712830,475043) : difference with theory (-27) = 0 CORRECTING DEFECT 24 (vertices=90, convex hull=67, v0=130754) After retessellation of defect 24 (v0=130754), euler #=-26 (237775,712904,475103) : difference with theory (-26) = 0 CORRECTING DEFECT 25 (vertices=5, convex hull=26, v0=131953) After retessellation of defect 25 (v0=131953), euler #=-25 (237776,712913,475112) : difference with theory (-25) = 0 CORRECTING DEFECT 26 (vertices=27, convex hull=60, v0=134992) After retessellation of defect 26 (v0=134992), euler #=-24 (237785,712962,475153) : difference with theory (-24) = 0 CORRECTING DEFECT 27 (vertices=108, convex hull=54, v0=135404) After retessellation of defect 27 (v0=135404), euler #=-23 (237789,712994,475182) : difference with theory (-23) = 0 CORRECTING DEFECT 28 (vertices=12, convex hull=17, v0=136659) After retessellation of defect 28 (v0=136659), euler #=-22 (237790,713000,475188) : difference with theory (-22) = 0 CORRECTING DEFECT 29 (vertices=154, convex hull=100, v0=136676) After retessellation of defect 29 (v0=136676), euler #=-21 (237812,713118,475285) : difference with theory (-21) = 0 CORRECTING DEFECT 30 (vertices=102, convex hull=57, v0=138755) After retessellation of defect 30 (v0=138755), euler #=-20 (237817,713156,475319) : difference with theory (-20) = 0 CORRECTING DEFECT 31 (vertices=68, convex hull=66, v0=150053) After retessellation of defect 31 (v0=150053), euler #=-19 (237826,713214,475369) : difference with theory (-19) = 0 CORRECTING DEFECT 32 (vertices=39, convex hull=73, v0=152285) After retessellation of defect 32 (v0=152285), euler #=-18 (237836,713268,475414) : difference with theory (-18) = 0 CORRECTING DEFECT 33 (vertices=10, convex hull=29, v0=153747) After retessellation of defect 33 (v0=153747), euler #=-17 (237836,713276,475423) : difference with theory (-17) = 0 CORRECTING DEFECT 34 (vertices=32, convex hull=38, v0=164695) After retessellation of defect 34 (v0=164695), euler #=-16 (237839,713293,475438) : difference with theory (-16) = 0 CORRECTING DEFECT 35 (vertices=8, convex hull=20, v0=168338) After retessellation of defect 35 (v0=168338), euler #=-15 (237839,713298,475444) : difference with theory (-15) = 0 CORRECTING DEFECT 36 (vertices=100, convex hull=38, v0=169419) After retessellation of defect 36 (v0=169419), euler #=-14 (237849,713341,475478) : difference with theory (-14) = 0 CORRECTING DEFECT 37 (vertices=91, convex hull=34, v0=169588) After retessellation of defect 37 (v0=169588), euler #=-13 (237852,713363,475498) : difference with theory (-13) = 0 CORRECTING DEFECT 38 (vertices=40, convex hull=30, v0=172541) After retessellation of defect 38 (v0=172541), euler #=-12 (237855,713384,475517) : difference with theory (-12) = 0 CORRECTING DEFECT 39 (vertices=30, convex hull=59, v0=172595) After retessellation of defect 39 (v0=172595), euler #=-11 (237861,713423,475551) : difference with theory (-11) = 0 CORRECTING DEFECT 40 (vertices=37, convex hull=33, v0=173547) After retessellation of defect 40 (v0=173547), euler #=-10 (237866,713447,475571) : difference with theory (-10) = 0 CORRECTING DEFECT 41 (vertices=5, convex hull=33, v0=175288) After retessellation of defect 41 (v0=175288), euler #=-9 (237867,713462,475586) : difference with theory (-9) = 0 CORRECTING DEFECT 42 (vertices=23, convex hull=42, v0=176578) After retessellation of defect 42 (v0=176578), euler #=-8 (237871,713486,475607) : difference with theory (-8) = 0 CORRECTING DEFECT 43 (vertices=81, convex hull=31, v0=176659) After retessellation of defect 43 (v0=176659), euler #=-7 (237874,713505,475624) : difference with theory (-7) = 0 CORRECTING DEFECT 44 (vertices=21, convex hull=61, v0=176799) After retessellation of defect 44 (v0=176799), euler #=-6 (237881,713548,475661) : difference with theory (-6) = 0 CORRECTING DEFECT 45 (vertices=6, convex hull=27, v0=185701) After retessellation of defect 45 (v0=185701), euler #=-5 (237882,713560,475673) : difference with theory (-5) = 0 CORRECTING DEFECT 46 (vertices=16, convex hull=30, v0=188175) After retessellation of defect 46 (v0=188175), euler #=-4 (237883,713569,475682) : difference with theory (-4) = 0 CORRECTING DEFECT 47 (vertices=33, convex hull=38, v0=198472) After retessellation of defect 47 (v0=198472), euler #=-3 (237888,713597,475706) : difference with theory (-3) = 0 CORRECTING DEFECT 48 (vertices=28, convex hull=26, v0=200420) After retessellation of defect 48 (v0=200420), euler #=-2 (237892,713617,475723) : difference with theory (-2) = 0 CORRECTING DEFECT 49 (vertices=21, convex hull=20, v0=211628) After retessellation of defect 49 (v0=211628), euler #=-1 (237892,713622,475729) : difference with theory (-1) = 0 CORRECTING DEFECT 50 (vertices=24, convex hull=30, v0=216013) After retessellation of defect 50 (v0=216013), euler #=0 (237894,713635,475741) : difference with theory (0) = 0 CORRECTING DEFECT 51 (vertices=27, convex hull=19, v0=222306) After retessellation of defect 51 (v0=222306), euler #=1 (237895,713647,475753) : difference with theory (1) = 0 CORRECTING DEFECT 52 (vertices=51, convex hull=71, v0=225137) After retessellation of defect 52 (v0=225137), euler #=2 (237904,713706,475804) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.71 +- 0.17 (0.10-->6.25) (max @ vno 9268 --> 13299) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.71 +- 0.17 (0.10-->6.25) (max @ vno 9268 --> 13299) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 189 mutations (36.5%), 329 crossovers (63.5%), 29 vertices were eliminated building final representation... 2238 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=237904, nf=475804, ne=713706, g=0) writing corrected surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.1 minutes 0 defective edges removing intersecting faces 000: 239 intersecting 001: 10 intersecting mris_fix_topology utimesec 1575.515391 mris_fix_topology stimesec 0.644490 mris_fix_topology ru_maxrss 767276 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 375902 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 22376 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5397 mris_fix_topology ru_nivcsw 516 FSRUNTIME@ mris_fix_topology lh 0.4343 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 237904 - 713706 + 475804 = 2 --> 0 holes F =2V-4: 475804 = 475808-4 (0) 2E=3F: 1427412 = 1427412 (0) total defect index = 0 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 27 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat May 22 05:25:26 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-01 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-01/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/wm.mgz... 47176 bright wm thresholded. 800 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.orig... computing class statistics... border white: 469153 voxels (1.43%) border gray 502265 voxels (1.53%) WM (103.0): 102.4 +- 6.5 [70.0 --> 110.0] GM (82.0) : 81.0 +- 9.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.3 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 57.7 (was 40) setting MAX_GRAY to 102.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.3 (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 +- 0.17 (0.02-->2.57) (max @ vno 141258 --> 141278) face area 0.18 +- 0.08 (0.00-->1.53) mean absolute distance = 1.39 +- 1.50 7531 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=109+-3.5, GM=77+-6.1 mean inside = 100.8, mean outside = 82.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=95.0, 118 (118) missing vertices, mean dist -0.7 [2.1 (%49.8)->0.6 (%50.2))] %43 local maxima, %41 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg55, 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 (0.04-->3.20) (max @ vno 166223 --> 166258) face area 0.18 +- 0.08 (0.00-->1.39) mean absolute distance = 0.56 +- 0.76 8435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4959988.5, rms=9.271 001: dt: 0.5000, sse=2408174.8, rms=5.561 (40.013%) 002: dt: 0.5000, sse=1625841.5, rms=3.694 (33.571%) 003: dt: 0.5000, sse=1497942.9, rms=3.255 (11.894%) 004: dt: 0.5000, sse=1481697.2, rms=3.162 (2.859%) rms = 3.12, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=1459199.4, rms=3.121 (1.284%) 006: dt: 0.2500, sse=1178377.9, rms=1.839 (41.090%) 007: dt: 0.2500, sse=1125538.5, rms=1.482 (19.424%) 008: dt: 0.2500, sse=1110573.5, rms=1.386 (6.430%) 009: dt: 0.2500, sse=1105381.5, rms=1.300 (6.209%) 010: dt: 0.2500, sse=1091255.6, rms=1.244 (4.305%) rms = 1.21, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=1099858.6, rms=1.205 (3.133%) rms = 1.17, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=1083762.0, rms=1.173 (2.661%) 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=94.4, 178 (48) missing vertices, mean dist -0.2 [0.9 (%39.7)->0.3 (%60.3))] %82 local maxima, %11 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg55, 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 +- 0.18 (0.04-->3.64) (max @ vno 162015 --> 160665) face area 0.21 +- 0.09 (0.00-->2.12) mean absolute distance = 0.31 +- 0.54 10548 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1998852.5, rms=4.328 013: dt: 0.5000, sse=1534042.6, rms=2.885 (33.342%) rms = 2.91, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=1312712.5, rms=1.971 (31.686%) 015: dt: 0.2500, sse=1236727.9, rms=1.333 (32.335%) 016: dt: 0.2500, sse=1201464.5, rms=1.136 (14.829%) 017: dt: 0.2500, sse=1187087.8, rms=1.063 (6.436%) rms = 1.02, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=1196356.6, rms=1.019 (4.106%) rms = 0.98, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=1181399.4, rms=0.984 (3.465%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.4, 157 (29) missing vertices, mean dist -0.1 [0.5 (%35.8)->0.2 (%64.2))] %91 local maxima, % 4 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg55, 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 +- 0.18 (0.03-->3.65) (max @ vno 162015 --> 160665) face area 0.20 +- 0.09 (0.00-->2.53) mean absolute distance = 0.22 +- 0.41 6522 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1359951.2, rms=2.326 020: dt: 0.5000, sse=1348963.4, rms=2.180 (6.261%) rms = 2.65, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=1189606.2, rms=1.367 (37.300%) 022: dt: 0.2500, sse=1165465.2, rms=1.042 (23.785%) 023: dt: 0.2500, sse=1165119.0, rms=0.978 (6.119%) rms = 0.96, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=1148203.2, rms=0.957 (2.117%) rms = 0.91, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=1138982.1, rms=0.914 (4.529%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.1, 167 (20) missing vertices, mean dist -0.0 [0.4 (%30.2)->0.1 (%69.8))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg55, 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-01/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1212115.0, rms=1.553 rms = 1.52, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=1234487.9, rms=1.520 (2.146%) 027: dt: 0.2500, sse=1151715.9, rms=1.015 (33.221%) 028: dt: 0.2500, sse=1132931.1, rms=0.833 (17.920%) rms = 0.89, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=1121646.9, rms=0.778 (6.643%) 030: dt: 0.1250, sse=1120216.0, rms=0.725 (6.748%) rms = 0.71, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=1119443.1, rms=0.714 (1.546%) positioning took 0.8 minutes generating cortex label... 14 non-cortical segments detected only using segment with 12397 vertices erasing segment 1 (vno[0] = 127110) erasing segment 2 (vno[0] = 167630) erasing segment 3 (vno[0] = 168943) erasing segment 4 (vno[0] = 169884) erasing segment 5 (vno[0] = 174283) erasing segment 6 (vno[0] = 174294) erasing segment 7 (vno[0] = 174303) erasing segment 8 (vno[0] = 174321) erasing segment 9 (vno[0] = 175711) erasing segment 10 (vno[0] = 175715) erasing segment 11 (vno[0] = 176966) erasing segment 12 (vno[0] = 185774) erasing segment 13 (vno[0] = 215401) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.area vertex spacing 0.70 +- 0.19 (0.03-->3.62) (max @ vno 160665 --> 162015) face area 0.21 +- 0.09 (0.00-->2.86) refinement took 5.9 minutes #-------------------------------------------- #@# Smooth2 lh Sat May 22 05:31:18 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 Sat May 22 05:31:25 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_inflate -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated niterations = 50 Reading ../surf/lh.smoothwm avg radius = 48.0 mm, total surface area = 90466 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.153 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.067 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) step 065: RMS=0.019 (target=0.015) step 070: RMS=0.018 (target=0.015) step 075: RMS=0.018 (target=0.015) step 080: RMS=0.017 (target=0.015) step 085: RMS=0.016 (target=0.015) step 090: RMS=0.016 (target=0.015) step 095: RMS=0.016 (target=0.015) step 100: RMS=0.015 (target=0.015) step 105: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 202.308305 mris_inflate stimesec 1.828023 mris_inflate ru_maxrss 379404 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 686813 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 18600 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 84483 mris_inflate ru_nivcsw 193 #-------------------------------------------- #@# Curv .H and .K lh Sat May 22 05:32:03 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf mris_curvature -w lh.white.preaparc total integrated curvature = 30.793*4pi (386.957) --> -30 handles ICI = 241.8, FI = 2719.6, variation=41690.957 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 356 vertices thresholded to be in k1 ~ [-0.17 0.30], k2 ~ [-0.08 0.05] total integrated curvature = 0.663*4pi (8.335) --> 0 handles ICI = 1.5, FI = 9.0, variation=155.315 236 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 248 vertices thresholded to be in [-0.10 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Sat May 22 05:33:37 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-01 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-01/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 [ 425 ] Gb_filter = 0 WARN: S lookup min: -0.431083 WARN: S explicit min: 0.000000 vertex = 183 #-------------------------------------------- #@# Sphere lh Sat May 22 05:33:43 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_sphere -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 0.272... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=blg55, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.56 pass 1: epoch 2 of 3 starting distance error %20.54 unfolding complete - removing small folds... starting distance error %20.46 removing remaining folds... final distance error %20.47 MRISunfold() return, current seed 1234 -01: dt=0.0000, 279 negative triangles 140: dt=0.9900, 279 negative triangles 141: dt=0.9900, 123 negative triangles 142: dt=0.9900, 109 negative triangles 143: dt=0.9900, 83 negative triangles 144: dt=0.9900, 88 negative triangles 145: dt=0.9900, 76 negative triangles 146: dt=0.9900, 61 negative triangles 147: dt=0.9900, 50 negative triangles 148: dt=0.9900, 41 negative triangles 149: dt=0.9900, 38 negative triangles 150: dt=0.9900, 41 negative triangles 151: dt=0.9900, 35 negative triangles 152: dt=0.9900, 38 negative triangles 153: dt=0.9900, 38 negative triangles 154: dt=0.9900, 34 negative triangles 155: dt=0.9900, 32 negative triangles 156: dt=0.9900, 27 negative triangles 157: dt=0.9900, 27 negative triangles 158: dt=0.9900, 26 negative triangles 159: dt=0.9900, 29 negative triangles 160: dt=0.9900, 24 negative triangles 161: dt=0.9900, 24 negative triangles 162: dt=0.9900, 20 negative triangles 163: dt=0.9900, 17 negative triangles 164: dt=0.9900, 15 negative triangles 165: dt=0.9900, 12 negative triangles 166: dt=0.9900, 16 negative triangles 167: dt=0.9900, 11 negative triangles 168: dt=0.9900, 9 negative triangles 169: dt=0.9900, 6 negative triangles 170: dt=0.9900, 6 negative triangles 171: dt=0.9900, 7 negative triangles 172: dt=0.9900, 5 negative triangles 173: dt=0.9900, 4 negative triangles 174: dt=0.9900, 6 negative triangles 175: dt=0.9900, 3 negative triangles 176: dt=0.9900, 3 negative triangles 177: dt=0.9900, 3 negative triangles 178: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.21 hours mris_sphere utimesec 5127.047883 mris_sphere stimesec 3.795208 mris_sphere ru_maxrss 525080 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 1831630 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 16736 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 109420 mris_sphere ru_nivcsw 4825 FSRUNTIME@ mris_sphere 0.2066 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Sat May 22 05:46:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01/scripts cmdline mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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=blg55, 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=blg55, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.686 curvature mean = 0.028, std = 0.822 curvature mean = 0.019, std = 0.865 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 601041.9, tmin=1.2001 d=32.00 min @ (-8.00, 0.00, 8.00) sse = 483074.5, tmin=2.4104 d=16.00 min @ (0.00, -4.00, -8.00) sse = 442193.1, tmin=3.6295 d=8.00 min @ (0.00, 0.00, 2.00) sse = 431544.6, tmin=4.8563 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 427922.0, tmin=6.0849 d=2.00 min @ (0.00, 0.50, 0.00) sse = 427760.5, tmin=7.3255 d=1.00 min @ (0.00, -0.25, 0.25) sse = 427596.2, tmin=8.6414 d=0.50 min @ (0.12, 0.12, -0.12) sse = 427556.4, tmin=9.9594 tol=1.0e+00, sigma=0.5, host=blg55, 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 9.96 min curvature mean = 0.004, std = 0.828 curvature mean = 0.008, std = 0.947 curvature mean = -0.002, std = 0.833 curvature mean = 0.003, std = 0.978 curvature mean = -0.005, std = 0.832 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.033, std = 0.322 curvature mean = 0.040, std = 0.242 curvature mean = 0.052, std = 0.323 curvature mean = 0.038, std = 0.298 curvature mean = 0.027, std = 0.504 curvature mean = 0.037, std = 0.324 curvature mean = 0.015, std = 0.654 curvature mean = 0.038, std = 0.335 curvature mean = 0.006, std = 0.769 MRISregister() return, current seed 0 -01: dt=0.0000, 80 negative triangles 126: dt=0.9900, 80 negative triangles expanding nbhd size to 1 127: dt=0.9900, 107 negative triangles 128: dt=0.9900, 80 negative triangles 129: dt=0.9900, 85 negative triangles 130: dt=0.9900, 76 negative triangles 131: dt=0.9900, 77 negative triangles 132: dt=0.9900, 75 negative triangles 133: dt=0.9900, 68 negative triangles 134: dt=0.9900, 59 negative triangles 135: dt=0.9900, 60 negative triangles 136: dt=0.9900, 42 negative triangles 137: dt=0.9900, 43 negative triangles 138: dt=0.9900, 39 negative triangles 139: dt=0.9900, 37 negative triangles 140: dt=0.9900, 37 negative triangles 141: dt=0.9900, 35 negative triangles 142: dt=0.9900, 35 negative triangles 143: dt=0.9900, 27 negative triangles 144: dt=0.9900, 26 negative triangles 145: dt=0.9900, 24 negative triangles 146: dt=0.9900, 19 negative triangles 147: dt=0.9900, 20 negative triangles 148: dt=0.9900, 17 negative triangles 149: dt=0.9900, 15 negative triangles 150: dt=0.9900, 15 negative triangles 151: dt=0.9900, 17 negative triangles 152: dt=0.9900, 12 negative triangles 153: dt=0.9900, 9 negative triangles 154: dt=0.9900, 9 negative triangles 155: dt=0.9900, 10 negative triangles 156: dt=0.9900, 10 negative triangles 157: dt=0.9900, 9 negative triangles 158: dt=0.9900, 9 negative triangles 159: dt=0.9900, 9 negative triangles 160: dt=0.9900, 8 negative triangles 161: dt=0.9900, 9 negative triangles 162: dt=0.9900, 9 negative triangles 163: dt=0.9900, 8 negative triangles 164: dt=0.9900, 8 negative triangles 165: dt=0.9900, 9 negative triangles 166: dt=0.9900, 8 negative triangles 167: dt=0.9900, 8 negative triangles 168: dt=0.9900, 7 negative triangles 169: dt=0.9900, 7 negative triangles 170: dt=0.9900, 7 negative triangles 171: dt=0.9900, 7 negative triangles 172: dt=0.9900, 7 negative triangles 173: dt=0.9900, 9 negative triangles 174: dt=0.9900, 9 negative triangles 175: dt=0.9900, 7 negative triangles 176: dt=0.9900, 6 negative triangles 177: dt=0.9900, 6 negative triangles 178: dt=0.9900, 5 negative triangles 179: dt=0.9900, 5 negative triangles 180: dt=0.9900, 5 negative triangles 181: dt=0.9900, 5 negative triangles 182: dt=0.9900, 6 negative triangles 183: dt=0.9900, 6 negative triangles 184: dt=0.9900, 6 negative triangles 185: dt=0.9900, 4 negative triangles 186: dt=0.9900, 4 negative triangles 187: dt=0.9900, 2 negative triangles 188: dt=0.9900, 1 negative triangles 189: dt=0.9900, 1 negative triangles 190: dt=0.9900, 1 negative triangles 191: dt=0.9900, 1 negative triangles 192: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.59 hours mris_register utimesec 10158.815369 mris_register stimesec 6.811021 mris_register ru_maxrss 428844 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 3484396 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5580 mris_register ru_oublock 16736 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 123113 mris_register ru_nivcsw 9882 FSRUNTIME@ mris_register 0.5858 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Sat May 22 06:21:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 Sat May 22 06:21:19 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 Sat May 22 06:21:21 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 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... 2693 labels changed using aseg relabeling using gibbs priors... 000: 4845 changed, 237904 examined... 001: 1259 changed, 20118 examined... 002: 309 changed, 6788 examined... 003: 113 changed, 1842 examined... 004: 35 changed, 656 examined... 005: 18 changed, 229 examined... 006: 10 changed, 112 examined... 007: 6 changed, 49 examined... 008: 0 changed, 35 examined... 340 labels changed using aseg 000: 171 total segments, 124 labels (738 vertices) changed 001: 45 total segments, 6 labels (31 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 3702 vertices marked for relabeling... 3702 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 17 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat May 22 06:21:39 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-01 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-01/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/wm.mgz... 47176 bright wm thresholded. 800 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.orig... computing class statistics... border white: 469153 voxels (1.43%) border gray 502265 voxels (1.53%) WM (103.0): 102.4 +- 6.5 [70.0 --> 110.0] GM (82.0) : 81.0 +- 9.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.3 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 57.7 (was 40) setting MAX_GRAY to 102.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.3 (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=109+-3.5, GM=77+-6.1 mean inside = 100.8, mean outside = 82.7 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 (0.03-->3.62) (max @ vno 160665 --> 162015) face area 0.21 +- 0.09 (0.00-->2.86) mean absolute distance = 1.29 +- 1.36 6665 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 397 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 16 points - only 0.00% unknown deleting segment 7 with 47 points - only 0.00% unknown deleting segment 8 with 52 points - only 0.00% unknown deleting segment 9 with 128 points - only 0.00% unknown deleting segment 10 with 70 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=94.8, 129 (128) missing vertices, mean dist -0.5 [2.3 (%38.4)->0.5 (%61.6))] %42 local maxima, %42 large gradients and %12 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg55, 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-->3.70) (max @ vno 162015 --> 160665) face area 0.21 +- 0.09 (0.00-->3.23) mean absolute distance = 0.54 +- 0.76 8186 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2498385.0, rms=5.531 001: dt: 0.5000, sse=1554353.6, rms=3.118 (43.615%) 002: dt: 0.5000, sse=1465010.6, rms=2.809 (9.909%) rms = 2.89, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=1261747.4, rms=1.865 (33.607%) 004: dt: 0.2500, sse=1195766.4, rms=1.342 (28.062%) 005: dt: 0.2500, sse=1183137.1, rms=1.214 (9.556%) 006: dt: 0.2500, sse=1173336.9, rms=1.157 (4.684%) rms = 1.13, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=1172083.1, rms=1.133 (2.062%) rms = 1.10, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=1171630.8, rms=1.096 (3.274%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 395 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 23 points - only 0.00% unknown deleting segment 5 with 36 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown deleting segment 7 with 109 points - only 0.00% unknown deleting segment 8 with 72 points - only 0.00% unknown deleting segment 9 with 32 points - only 0.00% unknown mean border=94.3, 124 (45) missing vertices, mean dist -0.2 [0.9 (%39.4)->0.3 (%60.6))] %82 local maxima, %11 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg55, 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 +- 0.18 (0.03-->3.68) (max @ vno 162015 --> 160665) face area 0.21 +- 0.10 (0.00-->3.67) mean absolute distance = 0.30 +- 0.53 10434 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1916438.0, rms=4.117 009: dt: 0.5000, sse=1497613.5, rms=2.779 (32.495%) rms = 2.87, time step reduction 1 of 3 to 0.250... 010: dt: 0.2500, sse=1287002.5, rms=1.852 (33.365%) 011: dt: 0.2500, sse=1210324.1, rms=1.244 (32.806%) 012: dt: 0.2500, sse=1188955.6, rms=1.075 (13.635%) 013: dt: 0.2500, sse=1195718.8, rms=1.022 (4.943%) rms = 0.99, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=1178396.5, rms=0.994 (2.692%) rms = 0.96, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=1181274.9, rms=0.957 (3.703%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 392 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 36 points - only 0.00% unknown deleting segment 4 with 39 points - only 0.00% unknown deleting segment 5 with 123 points - only 0.00% unknown deleting segment 6 with 69 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown mean border=94.4, 151 (25) missing vertices, mean dist -0.1 [0.5 (%36.2)->0.2 (%63.8))] %91 local maxima, % 4 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg55, 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 +- 0.18 (0.04-->3.75) (max @ vno 162015 --> 160665) face area 0.21 +- 0.09 (0.00-->3.87) mean absolute distance = 0.22 +- 0.41 6583 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1353982.1, rms=2.293 016: dt: 0.5000, sse=1331729.9, rms=2.173 (5.233%) rms = 2.63, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=1188491.8, rms=1.355 (37.630%) 018: dt: 0.2500, sse=1159042.8, rms=1.020 (24.735%) 019: dt: 0.2500, sse=1154994.6, rms=0.956 (6.271%) rms = 0.94, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=1145897.6, rms=0.939 (1.782%) rms = 0.89, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=1144569.9, rms=0.894 (4.789%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 371 points - only 0.00% unknown deleting segment 2 with 29 points - only 0.00% unknown deleting segment 3 with 40 points - only 0.00% unknown deleting segment 4 with 137 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 66 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown mean border=94.1, 188 (22) missing vertices, mean dist -0.0 [0.4 (%30.4)->0.1 (%69.6))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg55, 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-01/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1210234.1, rms=1.502 rms = 1.50, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=1228240.1, rms=1.501 (0.049%) 023: dt: 0.2500, sse=1146990.0, rms=0.995 (33.712%) 024: dt: 0.2500, sse=1133105.0, rms=0.814 (18.182%) rms = 0.87, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=1122365.8, rms=0.759 (6.769%) rms = 0.71, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=1120123.5, rms=0.710 (6.518%) positioning took 0.7 minutes generating cortex label... 16 non-cortical segments detected only using segment with 12359 vertices erasing segment 1 (vno[0] = 90463) erasing segment 2 (vno[0] = 127110) erasing segment 3 (vno[0] = 142597) erasing segment 4 (vno[0] = 160802) erasing segment 5 (vno[0] = 164777) erasing segment 6 (vno[0] = 168943) erasing segment 7 (vno[0] = 169884) erasing segment 8 (vno[0] = 174283) erasing segment 9 (vno[0] = 174294) erasing segment 10 (vno[0] = 174303) erasing segment 11 (vno[0] = 174321) erasing segment 12 (vno[0] = 175710) erasing segment 13 (vno[0] = 176966) erasing segment 14 (vno[0] = 179778) erasing segment 15 (vno[0] = 185774) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.area vertex spacing 0.70 +- 0.19 (0.01-->3.58) (max @ vno 160665 --> 162015) face area 0.21 +- 0.09 (0.00-->3.87) 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 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 87 points - only 0.00% unknown deleting segment 3 with 30 points - only 0.00% unknown deleting segment 4 with 45 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 18 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 22 points - only 0.00% unknown deleting segment 11 with 149 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown deleting segment 14 with 17 points - only 0.00% unknown deleting segment 15 with 19 points - only 0.00% unknown deleting segment 17 with 16 points - only 0.00% unknown deleting segment 18 with 44 points - only 0.00% unknown deleting segment 19 with 10 points - only 0.00% unknown deleting segment 20 with 9 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=76.1, 137 (137) missing vertices, mean dist 0.8 [0.8 (%0.0)->1.0 (%100.0))] %18 local maxima, %52 large gradients and %25 min vals, 47 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg55, 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=17804696.0, rms=19.167 001: dt: 0.0500, sse=13583708.0, rms=16.571 (13.541%) 002: dt: 0.0500, sse=11410525.0, rms=15.061 (9.113%) 003: dt: 0.0500, sse=10042974.0, rms=14.027 (6.864%) 004: dt: 0.0500, sse=9074406.0, rms=13.246 (5.569%) 005: dt: 0.0500, sse=8332064.0, rms=12.615 (4.768%) 006: dt: 0.0500, sse=7733538.0, rms=12.081 (4.228%) 007: dt: 0.0500, sse=7231374.5, rms=11.615 (3.862%) 008: dt: 0.0500, sse=6798441.5, rms=11.197 (3.599%) 009: dt: 0.0500, sse=6417724.5, rms=10.816 (3.403%) 010: dt: 0.0500, sse=6078309.0, rms=10.464 (3.251%) positioning took 1.2 minutes mean border=69.8, 72 (42) missing vertices, mean dist 0.9 [0.2 (%0.0)->1.2 (%100.0))] %19 local maxima, %52 large gradients and %24 min vals, 93 gradients ignored tol=1.0e-04, sigma=2.0, host=blg55, 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=13877510.0, rms=16.760 011: dt: 0.0500, sse=13257709.0, rms=16.348 (2.460%) 012: dt: 0.0500, sse=12717928.0, rms=15.980 (2.250%) 013: dt: 0.0500, sse=12242603.0, rms=15.649 (2.072%) 014: dt: 0.0500, sse=11819428.0, rms=15.348 (1.923%) 015: dt: 0.0500, sse=11439002.0, rms=15.072 (1.797%) 016: dt: 0.0500, sse=11093556.0, rms=14.817 (1.692%) 017: dt: 0.0500, sse=10776771.0, rms=14.580 (1.605%) 018: dt: 0.0500, sse=10480982.0, rms=14.354 (1.548%) 019: dt: 0.0500, sse=10197632.0, rms=14.134 (1.529%) 020: dt: 0.0500, sse=9923619.0, rms=13.919 (1.524%) positioning took 1.2 minutes mean border=67.5, 87 (32) missing vertices, mean dist 0.9 [0.1 (%0.2)->1.2 (%99.8))] %19 local maxima, %52 large gradients and %24 min vals, 128 gradients ignored tol=1.0e-04, sigma=2.0, host=blg55, 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=11566255.0, rms=15.171 021: dt: 0.0500, sse=11210297.0, rms=14.910 (1.724%) 022: dt: 0.0500, sse=10878345.0, rms=14.661 (1.664%) 023: dt: 0.0500, sse=10568124.0, rms=14.426 (1.609%) 024: dt: 0.0500, sse=10276874.0, rms=14.200 (1.560%) 025: dt: 0.0500, sse=10001983.0, rms=13.985 (1.520%) 026: dt: 0.0500, sse=9739618.0, rms=13.775 (1.497%) 027: dt: 0.0500, sse=9487932.0, rms=13.571 (1.480%) 028: dt: 0.0500, sse=9245287.0, rms=13.372 (1.471%) 029: dt: 0.0500, sse=9009361.0, rms=13.175 (1.473%) 030: dt: 0.0500, sse=8779488.0, rms=12.980 (1.479%) positioning took 1.2 minutes mean border=66.5, 115 (30) missing vertices, mean dist 0.8 [0.1 (%1.5)->1.0 (%98.5))] %19 local maxima, %52 large gradients and %24 min vals, 129 gradients ignored tol=1.0e-04, sigma=2.0, host=blg55, 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=9608684.0, rms=13.670 031: dt: 0.5000, sse=7893449.0, rms=12.199 (10.759%) 032: dt: 0.5000, sse=6549048.5, rms=10.910 (10.564%) 033: dt: 0.5000, sse=5324792.0, rms=9.603 (11.982%) 034: dt: 0.5000, sse=4398006.5, rms=8.470 (11.801%) 035: dt: 0.5000, sse=3676645.2, rms=7.477 (11.723%) 036: dt: 0.5000, sse=3257993.0, rms=6.833 (8.616%) 037: dt: 0.5000, sse=2981952.8, rms=6.374 (6.715%) 038: dt: 0.5000, sse=2866180.0, rms=6.170 (3.200%) 039: dt: 0.5000, sse=2764588.8, rms=5.987 (2.966%) rms = 5.94, time step reduction 1 of 3 to 0.250... 040: dt: 0.5000, sse=2740273.0, rms=5.940 (0.773%) 041: dt: 0.2500, sse=2384672.0, rms=5.181 (12.781%) 042: dt: 0.2500, sse=2304066.0, rms=5.003 (3.435%) rms = 5.01, time step reduction 2 of 3 to 0.125... 043: dt: 0.1250, sse=2260815.2, rms=4.901 (2.045%) 044: dt: 0.1250, sse=2203414.0, rms=4.760 (2.874%) rms = 4.73, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=2193346.8, rms=4.734 (0.547%) positioning took 2.2 minutes mean border=63.2, 2419 (12) missing vertices, mean dist 0.3 [0.2 (%16.3)->0.4 (%83.7))] %45 local maxima, %27 large gradients and %22 min vals, 119 gradients ignored tol=1.0e-04, sigma=1.0, host=blg55, 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=3723925.5, rms=7.062 046: dt: 0.5000, sse=3537507.8, rms=6.736 (4.607%) 047: dt: 0.5000, sse=3193259.5, rms=6.167 (8.445%) 048: dt: 0.5000, sse=3142710.5, rms=6.051 (1.892%) 049: dt: 0.5000, sse=2823538.5, rms=5.451 (9.912%) 050: dt: 0.5000, sse=2786534.5, rms=5.352 (1.823%) 051: dt: 0.5000, sse=2545126.5, rms=4.846 (9.448%) rms = 4.94, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=2079654.6, rms=3.534 (27.074%) 053: dt: 0.2500, sse=1949028.0, rms=3.047 (13.775%) 054: dt: 0.2500, sse=1924642.0, rms=2.955 (3.027%) 055: dt: 0.2500, sse=1911904.0, rms=2.904 (1.706%) rms = 2.91, time step reduction 2 of 3 to 0.125... 056: dt: 0.1250, sse=1842998.4, rms=2.613 (10.049%) 057: dt: 0.1250, sse=1750070.9, rms=2.159 (17.351%) 058: dt: 0.1250, sse=1731131.5, rms=2.060 (4.602%) rms = 2.03, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1725561.5, rms=2.031 (1.389%) positioning took 2.5 minutes mean border=61.4, 3099 (5) missing vertices, mean dist 0.1 [0.2 (%20.0)->0.2 (%80.0))] %54 local maxima, %19 large gradients and %21 min vals, 109 gradients ignored tol=1.0e-04, sigma=0.5, host=blg55, 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=2084665.9, rms=3.316 rms = 4.85, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1912523.9, rms=2.655 (19.914%) 061: dt: 0.2500, sse=1871954.8, rms=2.467 (7.082%) rms = 2.51, time step reduction 2 of 3 to 0.125... 062: dt: 0.1250, sse=1854312.2, rms=2.383 (3.423%) 063: dt: 0.1250, sse=1829314.4, rms=2.264 (4.995%) 064: dt: 0.1250, sse=1818349.5, rms=2.212 (2.292%) rms = 2.19, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1812306.8, rms=2.185 (1.204%) positioning took 1.2 minutes mean border=60.6, 6050 (2) missing vertices, mean dist 0.0 [0.2 (%27.4)->0.1 (%72.6))] %56 local maxima, %17 large gradients and %20 min vals, 86 gradients ignored tol=1.0e-04, sigma=0.2, host=blg55, 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-01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1871690.5, rms=2.442 rms = 3.61, time step reduction 1 of 3 to 0.250... 066: dt: 0.2500, sse=1829523.4, rms=2.231 (8.649%) rms = 2.21, time step reduction 2 of 3 to 0.125... 067: dt: 0.2500, sse=1821119.0, rms=2.209 (0.996%) 068: dt: 0.1250, sse=1801916.2, rms=2.101 (4.860%) rms = 2.05, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1791374.5, rms=2.052 (2.361%) positioning took 0.8 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.area.pial vertex spacing 0.80 +- 0.36 (0.06-->7.43) (max @ vno 170610 --> 170625) face area 0.26 +- 0.20 (0.00-->6.41) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 237904 vertices processed 25000 of 237904 vertices processed 50000 of 237904 vertices processed 75000 of 237904 vertices processed 100000 of 237904 vertices processed 125000 of 237904 vertices processed 150000 of 237904 vertices processed 175000 of 237904 vertices processed 200000 of 237904 vertices processed 225000 of 237904 vertices processed 0 of 237904 vertices processed 25000 of 237904 vertices processed 50000 of 237904 vertices processed 75000 of 237904 vertices processed 100000 of 237904 vertices processed 125000 of 237904 vertices processed 150000 of 237904 vertices processed 175000 of 237904 vertices processed 200000 of 237904 vertices processed 225000 of 237904 vertices processed thickness calculation complete, 169:470 truncations. 40660 vertices at 0 distance 138427 vertices at 1 distance 150203 vertices at 2 distance 82093 vertices at 3 distance 30489 vertices at 4 distance 8962 vertices at 5 distance 2620 vertices at 6 distance 891 vertices at 7 distance 338 vertices at 8 distance 158 vertices at 9 distance 86 vertices at 10 distance 59 vertices at 11 distance 38 vertices at 12 distance 39 vertices at 13 distance 31 vertices at 14 distance 23 vertices at 15 distance 21 vertices at 16 distance 16 vertices at 17 distance 5 vertices at 18 distance 5 vertices at 19 distance 6 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.thickness positioning took 17.7 minutes #-------------------------------------------- #@# Surf Volume lh Sat May 22 06:39:23 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01 lh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label Total face volume 273429 Total vertex volume 270655 (mask=0) #@# sub-01 lh 270655 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 lh Sat May 22 06:39:28 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 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... 78 labels changed using aseg relabeling using gibbs priors... 000: 14449 changed, 237904 examined... 001: 3519 changed, 55742 examined... 002: 1229 changed, 18256 examined... 003: 504 changed, 6750 examined... 004: 256 changed, 2865 examined... 005: 142 changed, 1468 examined... 006: 72 changed, 793 examined... 007: 28 changed, 382 examined... 008: 21 changed, 162 examined... 009: 15 changed, 116 examined... 010: 1 changed, 59 examined... 011: 0 changed, 11 examined... 0 labels changed using aseg 000: 401 total segments, 313 labels (5162 vertices) changed 001: 107 total segments, 19 labels (44 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 77 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2463 vertices marked for relabeling... 2463 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Cortical Parc 3 lh Sat May 22 06:39:50 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 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... 2317 labels changed using aseg relabeling using gibbs priors... 000: 2866 changed, 237904 examined... 001: 684 changed, 13292 examined... 002: 221 changed, 3898 examined... 003: 93 changed, 1308 examined... 004: 67 changed, 573 examined... 005: 44 changed, 351 examined... 006: 26 changed, 211 examined... 007: 20 changed, 128 examined... 008: 18 changed, 100 examined... 009: 11 changed, 77 examined... 010: 12 changed, 59 examined... 011: 7 changed, 65 examined... 012: 3 changed, 48 examined... 013: 3 changed, 21 examined... 014: 2 changed, 21 examined... 015: 2 changed, 14 examined... 016: 2 changed, 14 examined... 017: 1 changed, 14 examined... 018: 1 changed, 7 examined... 019: 0 changed, 7 examined... 399 labels changed using aseg 000: 65 total segments, 32 labels (472 vertices) changed 001: 34 total segments, 1 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1940 vertices marked for relabeling... 1940 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# WM/GM Contrast lh Sat May 22 06:40:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts pctsurfcon --s sub-01 --lh-only Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts/pctsurfcon.log Sat May 22 06:40:08 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-01/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux blg5521.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-01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/tmp.pctsurfcon.116658/lh.wm.mgh --regheader sub-01 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00003; 0.00000 -1.00000 0.00000 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 = 127941 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/tmp.pctsurfcon.116658/lh.wm.mgh Dim: 237904 1 1 mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/tmp.pctsurfcon.116658/lh.gm.mgh --projfrac 0.3 --regheader sub-01 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 -0.00003; 0.00000 -1.00000 0.00000 0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white Done reading source surface Reading thickness /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 = 151451 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/tmp.pctsurfcon.116658/lh.gm.mgh Dim: 237904 1 1 mri_concat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/tmp.pctsurfcon.116658/lh.wm.mgh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/tmp.pctsurfcon.116658/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01/surf/lh.w-g.pct.mgh mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.w-g.pct.mgh --annot sub-01 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01/surf/lh.w-g.pct.mgh --annot sub-01 lh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/stats/lh.w-g.pct.stats --snr sysname Linux hostname blg5521.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-01/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-01/surf/lh.w-g.pct.mgh Vertex Area is 0.410615 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 Sat May 22 04:55:04 UTC 2021 Ended at Sat May 22 06:40:22 UTC 2021 #@#%# recon-all-run-time-hours 1.755 recon-all -s sub-01 finished without error at Sat May 22 06:40:24 UTC 2021 New invocation of recon-all Sat May 22 07:59:23 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-01 -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-01 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 blg5521.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 767932 maxlocks unlimited maxsignal 767932 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638260 53545396 132587636 2249344 10505228 137493016 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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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: 2021/05/22-07:59:23-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: blg5521.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 Sat May 22 07:59:24 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 282867 Total vertex volume 279909 (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) = 1608862 mm^3 (det: 1.210859 ) lhCtxGM: 275672.380 544356.000 diff=-268683.6 pctdiff=-97.465 rhCtxGM: 267632.289 525408.000 diff=-257775.7 pctdiff=-96.317 lhCtxWM: 181349.195 419340.000 diff=-237990.8 pctdiff=-131.233 rhCtxWM: 184010.119 421058.000 diff=-237047.9 pctdiff=-128.823 SubCortGMVol 112077.000 SupraTentVol 1049883.984 (2065053.000) diff=-1015169.016 pctdiff=-96.693 SupraTentVolNotVent 1007110.984 (2022280.000) diff=-1015169.016 pctdiff=-100.800 BrainSegVol 2367218.000 (2362345.000) diff=4873.000 pctdiff=0.206 BrainSegVolNotVent 2316992.000 (1315317.984) diff=1001674.016 pctdiff=43.232 BrainSegVolNotVent 2316992.000 CerebellumVol 294536.000 VentChorVol 42773.000 3rd4th5thCSF 7453.000 CSFVol 2580.000, OptChiasmVol 176.000 MaskVol 2927526.000 2590 1128 2796 2.626 0.361 0.071 0.014 14 1.5 bankssts 2051 817 2729 2.577 1.017 0.100 0.024 30 2.1 caudalanteriorcingulate 4126 1713 5396 2.860 0.431 0.077 0.016 30 2.8 caudalmiddlefrontal 4064 1535 4036 2.256 0.403 0.100 0.029 58 5.2 cuneus 1155 446 2215 3.390 0.902 0.080 0.031 9 1.8 entorhinal 8140 3466 11493 2.839 0.638 0.085 0.021 79 7.3 fusiform 12582 5266 14837 2.520 0.454 0.084 0.019 135 10.3 inferiorparietal 9813 4063 14684 2.865 0.638 0.090 0.024 120 10.1 inferiortemporal 2936 1172 2959 2.106 0.910 0.094 0.027 40 3.2 isthmuscingulate 12769 4957 13673 2.348 0.501 0.099 0.027 176 14.4 lateraloccipital 6460 2736 9126 2.865 0.547 0.097 0.026 83 7.3 lateralorbitofrontal 8676 3438 8919 2.285 0.599 0.098 0.032 108 13.0 lingual 5443 2156 6948 2.833 0.669 0.096 0.033 89 7.8 medialorbitofrontal 9998 4178 14859 2.768 0.667 0.089 0.024 134 9.9 middletemporal 1698 693 2418 2.843 0.679 0.064 0.016 8 1.1 parahippocampal 3650 1503 4800 2.805 0.544 0.084 0.020 33 2.9 paracentral 4191 1768 5534 2.749 0.466 0.087 0.021 47 3.8 parsopercularis 1876 757 2745 2.727 0.499 0.100 0.024 30 2.0 parsorbitalis 3365 1431 4076 2.565 0.486 0.081 0.018 37 2.4 parstriangularis 4301 1727 3250 2.096 0.469 0.080 0.023 33 4.5 pericalcarine 10330 4198 10752 2.290 0.463 0.079 0.017 95 7.4 postcentral 3005 1260 3761 2.513 0.809 0.104 0.030 51 3.8 posteriorcingulate 10651 4086 12622 2.808 0.453 0.075 0.026 99 10.9 precentral 10283 4301 12087 2.522 0.472 0.093 0.024 124 10.2 precuneus 1973 795 3117 2.998 0.823 0.104 0.036 36 3.1 rostralanteriorcingulate 16375 6801 20234 2.600 0.450 0.093 0.022 208 15.4 rostralmiddlefrontal 15961 6739 23756 2.986 0.564 0.087 0.021 146 14.1 superiorfrontal 16180 6593 16657 2.309 0.375 0.083 0.021 195 14.3 superiorparietal 9381 3907 12149 2.738 0.589 0.072 0.016 80 6.7 superiortemporal 12004 4977 14029 2.524 0.489 0.085 0.020 130 9.8 supramarginal 759 310 1406 2.950 0.488 0.143 0.048 21 1.7 frontalpole 921 416 2268 3.730 0.813 0.090 0.025 10 1.0 temporalpole 1390 468 1468 2.648 0.386 0.079 0.024 16 1.6 transversetemporal 5824 2447 8046 3.233 0.847 0.099 0.037 70 10.2 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-01 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 282867 Total vertex volume 279909 (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) = 1608862 mm^3 (det: 1.210859 ) lhCtxGM: 275672.380 544356.000 diff=-268683.6 pctdiff=-97.465 rhCtxGM: 267632.289 525408.000 diff=-257775.7 pctdiff=-96.317 lhCtxWM: 181349.195 419340.000 diff=-237990.8 pctdiff=-131.233 rhCtxWM: 184010.119 421058.000 diff=-237047.9 pctdiff=-128.823 SubCortGMVol 112077.000 SupraTentVol 1049883.984 (2065053.000) diff=-1015169.016 pctdiff=-96.693 SupraTentVolNotVent 1007110.984 (2022280.000) diff=-1015169.016 pctdiff=-100.800 BrainSegVol 2367218.000 (2362345.000) diff=4873.000 pctdiff=0.206 BrainSegVolNotVent 2316992.000 (1315317.984) diff=1001674.016 pctdiff=43.232 BrainSegVolNotVent 2316992.000 CerebellumVol 294536.000 VentChorVol 42773.000 3rd4th5thCSF 7453.000 CSFVol 2580.000, OptChiasmVol 176.000 MaskVol 2927526.000 2590 967 2796 2.626 0.361 0.067 0.020 26 1.9 bankssts 2051 1134 2729 2.577 1.017 0.090 0.022 34 2.1 caudalanteriorcingulate 4126 1942 5396 2.860 0.431 0.073 0.018 52 2.9 caudalmiddlefrontal 4064 1980 4036 2.256 0.403 0.091 0.024 50 4.2 cuneus 1155 807 2215 3.390 0.902 0.098 0.029 13 1.4 entorhinal 8140 4346 11493 2.839 0.638 0.093 0.032 154 13.7 fusiform 12582 6224 14837 2.520 0.454 0.086 0.021 119 11.0 inferiorparietal 9813 5533 14684 2.865 0.638 0.095 0.022 96 9.4 inferiortemporal 2936 1445 2959 2.106 0.910 0.085 0.024 26 2.7 isthmuscingulate 12769 6290 13673 2.348 0.501 0.088 0.021 154 10.6 lateraloccipital 6460 3400 9126 2.865 0.547 0.093 0.023 90 6.0 lateralorbitofrontal 8676 4225 8919 2.285 0.599 0.085 0.025 74 9.5 lingual 5443 2645 6948 2.833 0.669 0.088 0.026 78 5.4 medialorbitofrontal 9998 5976 14859 2.768 0.667 0.097 0.022 93 9.9 middletemporal 1698 996 2418 2.843 0.679 0.093 0.021 10 1.7 parahippocampal 3650 1783 4800 2.805 0.544 0.081 0.019 40 2.8 paracentral 4191 2143 5534 2.749 0.466 0.091 0.022 37 4.2 parsopercularis 1876 1153 2745 2.727 0.499 0.103 0.021 14 1.8 parsorbitalis 3365 1662 4076 2.565 0.486 0.089 0.021 39 3.0 parstriangularis 4301 1372 3250 2.096 0.469 0.066 0.019 58 3.4 pericalcarine 10330 5120 10752 2.290 0.463 0.078 0.015 65 6.6 postcentral 3005 1593 3761 2.513 0.809 0.099 0.031 72 4.8 posteriorcingulate 10651 4739 12622 2.808 0.453 0.070 0.019 130 7.9 precentral 10283 4990 12087 2.522 0.472 0.090 0.023 109 9.8 precuneus 1973 1208 3117 2.998 0.823 0.108 0.030 32 2.5 rostralanteriorcingulate 16375 8193 20234 2.600 0.450 0.091 0.022 185 14.8 rostralmiddlefrontal 15961 8584 23756 2.986 0.564 0.089 0.021 195 13.8 superiorfrontal 16180 7417 16657 2.309 0.375 0.079 0.017 140 11.4 superiorparietal 9381 4703 12149 2.738 0.589 0.085 0.019 76 8.0 superiortemporal 12004 5897 14029 2.524 0.489 0.087 0.022 113 11.7 supramarginal 759 601 1406 2.950 0.488 0.143 0.027 7 1.0 frontalpole 921 781 2268 3.730 0.813 0.114 0.018 4 0.9 temporalpole 1390 657 1468 2.648 0.386 0.069 0.014 6 0.9 transversetemporal 5824 2351 8046 3.233 0.847 0.104 0.084 1758 30.1 insula #----------------------------------------- #@# Parcellation Stats 2 lh Sat May 22 08:01:30 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01 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-01/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 282867 Total vertex volume 279909 (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) = 1608862 mm^3 (det: 1.210859 ) lhCtxGM: 275672.380 544356.000 diff=-268683.6 pctdiff=-97.465 rhCtxGM: 267632.289 525408.000 diff=-257775.7 pctdiff=-96.317 lhCtxWM: 181349.195 419340.000 diff=-237990.8 pctdiff=-131.233 rhCtxWM: 184010.119 421058.000 diff=-237047.9 pctdiff=-128.823 SubCortGMVol 112077.000 SupraTentVol 1049883.984 (2065053.000) diff=-1015169.016 pctdiff=-96.693 SupraTentVolNotVent 1007110.984 (2022280.000) diff=-1015169.016 pctdiff=-100.800 BrainSegVol 2367218.000 (2362345.000) diff=4873.000 pctdiff=0.206 BrainSegVolNotVent 2316992.000 (1315317.984) diff=1001674.016 pctdiff=43.232 BrainSegVolNotVent 2316992.000 CerebellumVol 294536.000 VentChorVol 42773.000 3rd4th5thCSF 7453.000 CSFVol 2580.000, OptChiasmVol 176.000 MaskVol 2927526.000 2274 948 2777 2.498 0.447 0.094 0.024 28 2.4 G&S_frontomargin 2508 1043 3449 2.623 0.515 0.100 0.025 33 2.5 G&S_occipital_inf 2798 1032 3482 2.611 0.558 0.086 0.028 34 3.1 G&S_paracentral 2509 1076 3263 2.546 0.407 0.099 0.024 38 2.5 G&S_subcentral 1652 694 2558 2.679 0.499 0.131 0.042 40 3.3 G&S_transv_frontopol 3515 1486 4802 3.011 0.619 0.087 0.027 41 4.1 G&S_cingul-Ant 2079 895 3102 3.016 0.561 0.089 0.023 21 1.9 G&S_cingul-Mid-Ant 2286 983 2934 2.809 0.458 0.089 0.024 26 2.3 G&S_cingul-Mid-Post 1163 475 2075 2.952 0.562 0.134 0.045 29 2.2 G_cingul-Post-dorsal 568 225 736 2.463 0.929 0.101 0.033 9 0.7 G_cingul-Post-ventral 3959 1412 3993 2.182 0.460 0.106 0.035 66 6.1 G_cuneus 2721 1123 4287 2.843 0.485 0.103 0.027 44 3.1 G_front_inf-Opercular 653 267 1142 2.900 0.456 0.111 0.029 12 0.8 G_front_inf-Orbital 1887 792 2880 2.669 0.466 0.109 0.028 40 2.2 G_front_inf-Triangul 8455 3425 13354 2.851 0.480 0.103 0.026 138 8.8 G_front_middle 11742 4863 20189 3.105 0.610 0.096 0.025 141 12.0 G_front_sup 1228 492 1866 3.416 0.823 0.108 0.043 21 2.4 G_Ins_lg&S_cent_ins 1173 477 2531 3.721 0.612 0.118 0.046 21 2.4 G_insular_short 4041 1657 5908 2.575 0.487 0.112 0.032 80 5.0 G_occipital_middle 2503 907 2417 2.181 0.398 0.095 0.042 58 5.0 G_occipital_sup 3246 1346 5875 3.124 0.584 0.102 0.028 48 3.9 G_oc-temp_lat-fusifor 6016 2245 6659 2.349 0.646 0.110 0.040 96 11.0 G_oc-temp_med-Lingual 2200 865 3862 3.209 0.826 0.079 0.030 19 3.2 G_oc-temp_med-Parahip 4050 1643 7144 2.999 0.540 0.105 0.030 78 5.3 G_orbital 4173 1709 6295 2.707 0.517 0.107 0.029 87 4.9 G_pariet_inf-Angular 5803 2338 8221 2.697 0.523 0.097 0.024 86 6.0 G_pariet_inf-Supramar 6227 2561 7794 2.404 0.432 0.099 0.024 104 6.1 G_parietal_sup 3767 1438 4425 2.334 0.504 0.086 0.020 45 3.1 G_postcentral 3932 1358 5346 2.981 0.462 0.082 0.035 50 5.2 G_precentral 5705 2341 8196 2.641 0.497 0.108 0.031 102 7.1 G_precuneus 1517 597 2593 2.896 0.525 0.127 0.047 47 3.4 G_rectus 1486 598 1784 3.054 0.936 0.107 0.054 22 3.7 G_subcallosal 1033 343 1227 2.656 0.415 0.071 0.023 13 1.0 G_temp_sup-G_T_transv 2942 1179 4939 2.871 0.549 0.101 0.027 52 3.2 G_temp_sup-Lateral 1388 600 2465 3.614 0.666 0.052 0.009 3 0.6 G_temp_sup-Plan_polar 1687 718 1931 2.557 0.446 0.060 0.014 9 1.0 G_temp_sup-Plan_tempo 5457 2236 9647 3.062 0.602 0.101 0.030 95 6.7 G_temporal_inf 5663 2308 9779 2.880 0.658 0.107 0.033 115 7.7 G_temporal_middle 648 276 611 2.549 0.481 0.053 0.008 1 0.2 Lat_Fis-ant-Horizont 623 254 632 2.804 0.453 0.071 0.017 2 0.5 Lat_Fis-ant-Vertical 2028 821 1742 2.572 0.446 0.073 0.020 10 1.9 Lat_Fis-post 3483 1152 3032 2.110 0.483 0.096 0.031 49 4.7 Pole_occipital 2900 1230 6122 3.351 0.753 0.093 0.027 37 3.6 Pole_temporal 4934 2122 4063 2.176 0.505 0.080 0.021 34 4.4 S_calcarine 4277 1805 3620 2.352 0.539 0.061 0.016 16 3.0 S_central 1802 782 1692 2.533 0.393 0.067 0.013 9 1.1 S_cingul-Marginalis 766 368 968 3.277 0.448 0.094 0.028 6 1.1 S_circular_insula_ant 2120 915 2203 2.801 0.822 0.060 0.015 6 1.5 S_circular_insula_inf 3294 1411 3196 2.814 0.513 0.072 0.017 14 2.5 S_circular_insula_sup 1602 690 1701 2.552 0.709 0.069 0.012 8 0.9 S_collat_transv_ant 912 371 815 2.485 0.416 0.094 0.023 6 1.0 S_collat_transv_post 3758 1606 3915 2.552 0.397 0.080 0.017 27 2.5 S_front_inf 3276 1386 2868 2.452 0.362 0.075 0.014 19 2.1 S_front_middle 3608 1547 3776 2.712 0.358 0.061 0.012 12 1.6 S_front_sup 857 365 664 2.243 0.304 0.069 0.010 3 0.5 S_interm_prim-Jensen 6340 2667 5508 2.298 0.287 0.068 0.012 34 3.4 S_intrapariet&P_trans 1921 812 1534 2.272 0.302 0.077 0.015 9 1.1 S_oc_middle&Lunatus 2956 1227 2416 2.256 0.279 0.070 0.013 14 1.5 S_oc_sup&transversal 1082 455 1008 2.410 0.479 0.086 0.016 8 0.8 S_occipital_ant 1682 731 1840 2.559 0.470 0.062 0.011 6 0.8 S_oc-temp_lat 4066 1775 3948 2.418 0.470 0.075 0.018 22 3.0 S_oc-temp_med&Lingual 897 391 708 2.183 0.280 0.074 0.011 3 0.6 S_orbital_lateral 961 391 782 2.374 0.479 0.073 0.013 4 0.5 S_orbital_med-olfact 2690 1144 3045 2.608 0.459 0.092 0.023 26 2.4 S_orbital-H_Shaped 3743 1555 3268 2.330 0.380 0.076 0.017 25 2.7 S_parieto_occipital 2768 1034 1150 1.398 0.532 0.090 0.021 39 2.2 S_pericallosal 6032 2538 5186 2.271 0.300 0.065 0.012 27 2.9 S_postcentral 2336 978 2232 2.606 0.328 0.066 0.013 10 1.2 S_precentral-inf-part 1492 656 1539 2.723 0.341 0.065 0.010 5 0.6 S_precentral-sup-part 1465 583 1376 2.631 0.582 0.077 0.018 9 1.1 S_suborbital 1854 784 1642 2.372 0.362 0.073 0.016 7 1.2 S_subparietal 3801 1599 3291 2.367 0.431 0.068 0.011 14 2.1 S_temporal_inf 11270 4841 11303 2.485 0.445 0.067 0.013 57 6.0 S_temporal_sup 687 289 582 2.449 0.287 0.067 0.011 3 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 lh Sat May 22 08:02:35 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01 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-01/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 282867 Total vertex volume 279909 (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) = 1608862 mm^3 (det: 1.210859 ) lhCtxGM: 275672.380 544356.000 diff=-268683.6 pctdiff=-97.465 rhCtxGM: 267632.289 525408.000 diff=-257775.7 pctdiff=-96.317 lhCtxWM: 181349.195 419340.000 diff=-237990.8 pctdiff=-131.233 rhCtxWM: 184010.119 421058.000 diff=-237047.9 pctdiff=-128.823 SubCortGMVol 112077.000 SupraTentVol 1049883.984 (2065053.000) diff=-1015169.016 pctdiff=-96.693 SupraTentVolNotVent 1007110.984 (2022280.000) diff=-1015169.016 pctdiff=-100.800 BrainSegVol 2367218.000 (2362345.000) diff=4873.000 pctdiff=0.206 BrainSegVolNotVent 2316992.000 (1315317.984) diff=1001674.016 pctdiff=43.232 BrainSegVolNotVent 2316992.000 CerebellumVol 294536.000 VentChorVol 42773.000 3rd4th5thCSF 7453.000 CSFVol 2580.000, OptChiasmVol 176.000 MaskVol 2927526.000 2663 1086 3355 2.607 0.937 0.095 0.023 34 2.4 caudalanteriorcingulate 4467 1858 5807 2.855 0.431 0.076 0.016 32 2.9 caudalmiddlefrontal 5453 2086 5485 2.269 0.408 0.096 0.028 71 6.5 cuneus 1003 390 2001 3.359 0.933 0.082 0.033 8 1.7 entorhinal 7602 3238 10517 2.798 0.639 0.086 0.022 73 6.9 fusiform 13087 5432 15272 2.503 0.448 0.084 0.020 146 10.9 inferiorparietal 9391 3904 14455 2.907 0.633 0.088 0.024 116 9.6 inferiortemporal 2947 1176 3026 2.161 0.914 0.097 0.028 42 3.4 isthmuscingulate 12624 4896 13428 2.333 0.500 0.098 0.027 171 13.9 lateraloccipital 7645 3219 10835 2.823 0.621 0.105 0.032 119 11.3 lateralorbitofrontal 8804 3482 9022 2.283 0.598 0.098 0.032 108 13.0 lingual 4231 1655 5825 2.850 0.684 0.101 0.035 80 6.5 medialorbitofrontal 12974 5471 18484 2.764 0.641 0.088 0.022 155 12.3 middletemporal 1776 728 2523 2.829 0.679 0.065 0.016 8 1.2 parahippocampal 4193 1740 5605 2.818 0.553 0.083 0.020 38 3.3 paracentral 4025 1694 5233 2.743 0.467 0.088 0.021 45 3.6 parsopercularis 1735 707 2544 2.958 0.479 0.087 0.021 19 1.6 parsorbitalis 4118 1765 5045 2.535 0.476 0.088 0.020 51 3.5 parstriangularis 4201 1691 3157 2.103 0.471 0.079 0.023 32 4.2 pericalcarine 11974 4888 12481 2.312 0.463 0.080 0.018 109 9.0 postcentral 3250 1363 3920 2.506 0.787 0.103 0.030 53 4.1 posteriorcingulate 10492 4016 12338 2.806 0.449 0.075 0.026 96 10.7 precentral 10189 4245 12159 2.508 0.490 0.094 0.025 128 10.1 precuneus 2858 1142 3733 2.900 0.778 0.097 0.035 42 4.1 rostralanteriorcingulate 11543 4790 14224 2.595 0.429 0.093 0.022 145 10.3 rostralmiddlefrontal 19352 8109 28462 2.921 0.578 0.089 0.022 202 18.3 superiorfrontal 13255 5428 13478 2.308 0.350 0.081 0.020 161 11.7 superiorparietal 12127 5090 16460 2.824 0.677 0.074 0.018 107 9.3 superiortemporal 10915 4522 12753 2.535 0.490 0.086 0.021 120 9.3 supramarginal 1396 473 1481 2.657 0.380 0.079 0.024 16 1.5 transversetemporal 4647 1969 6799 3.298 0.743 0.092 0.030 47 6.5 insula /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label #-------------------------------------------- #@# BA_exvivo Labels lh Sat May 22 08:03:39 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 1375 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 5504 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 3242 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 11151 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 476 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4553 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 1386 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 7369 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 1641 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 7425 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 686 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4756 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 2958 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 16547 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 1573 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 5754 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 2567 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 5989 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 5657 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 10298 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 8893 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 17007 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 1437 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 3455 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 364 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1654 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1532 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 329 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1343 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 913 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 3005 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1632 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 515 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2511 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 714 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 3033 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 293 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1842 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 1369 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8404 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 839 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2751 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 977 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 2128 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 4172 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 7577 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 3731 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 7065 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 308 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 821 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 552 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-01 --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-01 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-01/surf/lh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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 237904 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 566 mri_label2label: Done mris_label2annot --s sub-01 --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-01/label cmdline mris_label2annot --s sub-01 --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 blg5521.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-01 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-01/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 171086 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/label/lh.BA_exvivo.annot mris_label2annot --s sub-01 --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-01/label cmdline mris_label2annot --s sub-01 --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 blg5521.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-01 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-01/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 198893 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/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-01 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282867 Total vertex volume 279909 (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) = 1608862 mm^3 (det: 1.210859 ) lhCtxGM: 275672.380 544356.000 diff=-268683.6 pctdiff=-97.465 rhCtxGM: 267632.289 525408.000 diff=-257775.7 pctdiff=-96.317 lhCtxWM: 181349.195 419340.000 diff=-237990.8 pctdiff=-131.233 rhCtxWM: 184010.119 421058.000 diff=-237047.9 pctdiff=-128.823 SubCortGMVol 112077.000 SupraTentVol 1049883.984 (2065053.000) diff=-1015169.016 pctdiff=-96.693 SupraTentVolNotVent 1007110.984 (2022280.000) diff=-1015169.016 pctdiff=-100.800 BrainSegVol 2367218.000 (2362345.000) diff=4873.000 pctdiff=0.206 BrainSegVolNotVent 2316992.000 (1315317.984) diff=1001674.016 pctdiff=43.232 BrainSegVolNotVent 2316992.000 CerebellumVol 294536.000 VentChorVol 42773.000 3rd4th5thCSF 7453.000 CSFVol 2580.000, OptChiasmVol 176.000 MaskVol 2927526.000 1844 666 2177 2.352 0.471 0.098 0.025 28 1.9 BA1_exvivo 7622 3156 7441 2.342 0.336 0.072 0.014 55 4.4 BA2_exvivo 1338 573 1011 2.306 0.354 0.079 0.023 6 1.1 BA3a_exvivo 3708 1533 3389 2.011 0.439 0.073 0.015 30 2.4 BA3b_exvivo 2735 1001 3814 3.014 0.509 0.077 0.028 25 3.2 BA4a_exvivo 1744 667 1795 2.920 0.289 0.064 0.031 17 2.1 BA4p_exvivo 12181 4997 18502 3.009 0.530 0.082 0.021 109 10.7 BA6_exvivo 3909 1622 5221 2.697 0.435 0.091 0.022 49 3.5 BA44_exvivo 5218 2219 6449 2.543 0.475 0.092 0.022 70 4.8 BA45_exvivo 7262 2754 5736 2.042 0.495 0.086 0.028 76 8.8 V1_exvivo 14017 5341 14184 2.286 0.517 0.101 0.030 183 18.6 V2_exvivo 3326 1401 4338 2.582 0.558 0.092 0.020 39 2.8 MT_exvivo 884 349 1761 3.380 0.842 0.075 0.029 7 1.3 perirhinal_exvivo 1030 428 1671 3.171 0.808 0.072 0.018 6 0.8 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-01 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-01/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 282867 Total vertex volume 279909 (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) = 1608862 mm^3 (det: 1.210859 ) lhCtxGM: 275672.380 544356.000 diff=-268683.6 pctdiff=-97.465 rhCtxGM: 267632.289 525408.000 diff=-257775.7 pctdiff=-96.317 lhCtxWM: 181349.195 419340.000 diff=-237990.8 pctdiff=-131.233 rhCtxWM: 184010.119 421058.000 diff=-237047.9 pctdiff=-128.823 SubCortGMVol 112077.000 SupraTentVol 1049883.984 (2065053.000) diff=-1015169.016 pctdiff=-96.693 SupraTentVolNotVent 1007110.984 (2022280.000) diff=-1015169.016 pctdiff=-100.800 BrainSegVol 2367218.000 (2362345.000) diff=4873.000 pctdiff=0.206 BrainSegVolNotVent 2316992.000 (1315317.984) diff=1001674.016 pctdiff=43.232 BrainSegVolNotVent 2316992.000 CerebellumVol 294536.000 VentChorVol 42773.000 3rd4th5thCSF 7453.000 CSFVol 2580.000, OptChiasmVol 176.000 MaskVol 2927526.000 1192 409 1434 2.351 0.581 0.105 0.030 20 1.5 BA1_exvivo 2817 1141 3039 2.480 0.292 0.067 0.012 17 1.4 BA2_exvivo 1149 488 815 2.304 0.334 0.078 0.021 5 1.0 BA3a_exvivo 2192 914 1719 1.872 0.327 0.054 0.010 7 0.9 BA3b_exvivo 2507 916 3389 3.060 0.491 0.070 0.027 20 2.8 BA4a_exvivo 1453 547 1462 2.873 0.267 0.068 0.035 17 1.9 BA4p_exvivo 6815 2727 10409 3.019 0.519 0.084 0.024 67 6.8 BA6_exvivo 2542 1058 3527 2.719 0.419 0.095 0.023 33 2.4 BA44_exvivo 2103 909 2810 2.563 0.436 0.099 0.023 33 2.0 BA45_exvivo 7526 2892 6059 2.035 0.502 0.085 0.026 73 8.7 V1_exvivo 6977 2524 6270 2.153 0.454 0.107 0.036 101 10.9 V2_exvivo 817 347 922 2.385 0.448 0.085 0.018 9 0.6 MT_exvivo 405 173 848 3.436 0.683 0.057 0.011 1 0.2 perirhinal_exvivo 516 209 946 3.361 0.679 0.066 0.014 2 0.3 entorhinal_exvivo Started at Sat May 22 07:59:20 UTC 2021 Ended at Sat May 22 08:09:01 UTC 2021 #@#%# recon-all-run-time-hours 0.161 recon-all -s sub-01 finished without error at Sat May 22 08:09:01 UTC 2021