Tue May 25 20:58:32 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-03 -sd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer subjid sub-03 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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 29917128 161078164 1969316 5643140 162342148 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/25-20:58:33-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: blg5611.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 rh Tue May 25 20:58:33 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 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 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 550526: 0.001090) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 2548 vertices, 2714 faces slice 60: 10532 vertices, 10898 faces slice 70: 22709 vertices, 23136 faces slice 80: 36249 vertices, 36753 faces slice 90: 52365 vertices, 52955 faces slice 100: 70046 vertices, 70619 faces slice 110: 85937 vertices, 86418 faces slice 120: 101669 vertices, 102236 faces slice 130: 119314 vertices, 119913 faces slice 140: 137025 vertices, 137613 faces slice 150: 153091 vertices, 153639 faces slice 160: 167814 vertices, 168420 faces slice 170: 183049 vertices, 183637 faces slice 180: 197011 vertices, 197524 faces slice 190: 208738 vertices, 209201 faces slice 200: 219705 vertices, 220154 faces slice 210: 229556 vertices, 229972 faces slice 220: 238904 vertices, 239327 faces slice 230: 247183 vertices, 247574 faces slice 240: 254140 vertices, 254444 faces slice 250: 258420 vertices, 258539 faces slice 260: 258622 vertices, 258704 faces slice 270: 258622 vertices, 258704 faces slice 280: 258622 vertices, 258704 faces slice 290: 258622 vertices, 258704 faces slice 300: 258622 vertices, 258704 faces slice 310: 258622 vertices, 258704 faces slice 320: 258622 vertices, 258704 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.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-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 258622 voxel in cpt #1: X=-82 [v=258622,e=776112,f=517408] located at (27.441891, -17.474520, 31.152311) For the whole surface: X=-82 [v=258622,e=776112,f=517408] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue May 25 20:58:40 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Tue May 25 20:58:49 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_inflate -no-save-sulc -n 50 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix niterations = 50 Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.0 mm, total surface area = 90663 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.7 minutes step 000: RMS=0.143 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) step 065: RMS=0.038 (target=0.015) step 070: RMS=0.037 (target=0.015) step 075: RMS=0.037 (target=0.015) step 080: RMS=0.037 (target=0.015) step 085: RMS=0.036 (target=0.015) step 090: RMS=0.036 (target=0.015) step 095: RMS=0.036 (target=0.015) step 100: RMS=0.036 (target=0.015) step 105: RMS=0.036 (target=0.015) step 110: RMS=0.036 (target=0.015) step 115: RMS=0.036 (target=0.015) step 120: RMS=0.036 (target=0.015) step 125: RMS=0.036 (target=0.015) step 130: RMS=0.036 (target=0.015) step 135: RMS=0.036 (target=0.015) step 140: RMS=0.036 (target=0.015) step 145: RMS=0.036 (target=0.015) step 150: RMS=0.036 (target=0.015) step 155: RMS=0.036 (target=0.015) step 160: RMS=0.036 (target=0.015) step 165: RMS=0.036 (target=0.015) step 170: RMS=0.037 (target=0.015) step 175: RMS=0.036 (target=0.015) step 180: RMS=0.036 (target=0.015) step 185: RMS=0.036 (target=0.015) step 190: RMS=0.036 (target=0.015) step 195: RMS=0.036 (target=0.015) step 200: RMS=0.036 (target=0.015) step 205: RMS=0.037 (target=0.015) step 210: RMS=0.037 (target=0.015) step 215: RMS=0.037 (target=0.015) step 220: RMS=0.037 (target=0.015) step 225: RMS=0.037 (target=0.015) step 230: RMS=0.037 (target=0.015) step 235: RMS=0.037 (target=0.015) step 240: RMS=0.037 (target=0.015) step 245: RMS=0.037 (target=0.015) step 250: RMS=0.037 (target=0.015) step 255: RMS=0.038 (target=0.015) step 260: RMS=0.040 (target=0.015) step 265: RMS=0.040 (target=0.015) step 270: RMS=0.040 (target=0.015) step 275: RMS=0.040 (target=0.015) step 280: RMS=0.040 (target=0.015) step 285: RMS=0.040 (target=0.015) step 290: RMS=0.040 (target=0.015) step 295: RMS=0.040 (target=0.015) step 300: RMS=0.040 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 469.262462 mris_inflate stimesec 2.084811 mris_inflate ru_maxrss 411476 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 828930 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 18192 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 102785 mris_inflate ru_nivcsw 406 #-------------------------------------------- #@# QSphere rh Tue May 25 21:00:29 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 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 0.71 +- 0.41 (0.00-->6.73) (max @ vno 113727 --> 115360) face area 0.01 +- 0.02 (-0.12-->0.59) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.281... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.450, avgs=0 005/300: dt: 0.9000, rms radial error=175.192, avgs=0 010/300: dt: 0.9000, rms radial error=174.638, avgs=0 015/300: dt: 0.9000, rms radial error=173.907, avgs=0 020/300: dt: 0.9000, rms radial error=173.073, avgs=0 025/300: dt: 0.9000, rms radial error=172.179, avgs=0 030/300: dt: 0.9000, rms radial error=171.253, avgs=0 035/300: dt: 0.9000, rms radial error=170.310, avgs=0 040/300: dt: 0.9000, rms radial error=169.360, avgs=0 045/300: dt: 0.9000, rms radial error=168.410, avgs=0 050/300: dt: 0.9000, rms radial error=167.461, avgs=0 055/300: dt: 0.9000, rms radial error=166.515, avgs=0 060/300: dt: 0.9000, rms radial error=165.573, avgs=0 065/300: dt: 0.9000, rms radial error=164.639, avgs=0 070/300: dt: 0.9000, rms radial error=163.710, avgs=0 075/300: dt: 0.9000, rms radial error=162.785, avgs=0 080/300: dt: 0.9000, rms radial error=161.866, avgs=0 085/300: dt: 0.9000, rms radial error=160.952, avgs=0 090/300: dt: 0.9000, rms radial error=160.043, avgs=0 095/300: dt: 0.9000, rms radial error=159.139, avgs=0 100/300: dt: 0.9000, rms radial error=158.239, avgs=0 105/300: dt: 0.9000, rms radial error=157.345, avgs=0 110/300: dt: 0.9000, rms radial error=156.456, avgs=0 115/300: dt: 0.9000, rms radial error=155.572, avgs=0 120/300: dt: 0.9000, rms radial error=154.693, avgs=0 125/300: dt: 0.9000, rms radial error=153.819, avgs=0 130/300: dt: 0.9000, rms radial error=152.950, avgs=0 135/300: dt: 0.9000, rms radial error=152.086, avgs=0 140/300: dt: 0.9000, rms radial error=151.226, avgs=0 145/300: dt: 0.9000, rms radial error=150.372, avgs=0 150/300: dt: 0.9000, rms radial error=149.522, avgs=0 155/300: dt: 0.9000, rms radial error=148.676, avgs=0 160/300: dt: 0.9000, rms radial error=147.836, avgs=0 165/300: dt: 0.9000, rms radial error=146.999, avgs=0 170/300: dt: 0.9000, rms radial error=146.168, avgs=0 175/300: dt: 0.9000, rms radial error=145.341, avgs=0 180/300: dt: 0.9000, rms radial error=144.519, avgs=0 185/300: dt: 0.9000, rms radial error=143.702, avgs=0 190/300: dt: 0.9000, rms radial error=142.889, avgs=0 195/300: dt: 0.9000, rms radial error=142.081, avgs=0 200/300: dt: 0.9000, rms radial error=141.277, avgs=0 205/300: dt: 0.9000, rms radial error=140.478, avgs=0 210/300: dt: 0.9000, rms radial error=139.683, avgs=0 215/300: dt: 0.9000, rms radial error=138.894, avgs=0 220/300: dt: 0.9000, rms radial error=138.108, avgs=0 225/300: dt: 0.9000, rms radial error=137.327, avgs=0 230/300: dt: 0.9000, rms radial error=136.551, avgs=0 235/300: dt: 0.9000, rms radial error=135.779, avgs=0 240/300: dt: 0.9000, rms radial error=135.011, avgs=0 245/300: dt: 0.9000, rms radial error=134.248, avgs=0 250/300: dt: 0.9000, rms radial error=133.489, avgs=0 255/300: dt: 0.9000, rms radial error=132.734, avgs=0 260/300: dt: 0.9000, rms radial error=131.984, avgs=0 265/300: dt: 0.9000, rms radial error=131.238, avgs=0 270/300: dt: 0.9000, rms radial error=130.496, avgs=0 275/300: dt: 0.9000, rms radial error=129.758, avgs=0 280/300: dt: 0.9000, rms radial error=129.024, avgs=0 285/300: dt: 0.9000, rms radial error=128.295, avgs=0 290/300: dt: 0.9000, rms radial error=127.570, avgs=0 295/300: dt: 0.9000, rms radial error=126.848, avgs=0 300/300: dt: 0.9000, rms radial error=126.131, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 32599.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 2 (K=40.0), pass 1, starting sse = 6343.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 820.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00141 epoch 4 (K=640.0), pass 1, starting sse = 66.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00457 final distance error %26.53 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 550.366606 mris_sphere stimesec 1.826595 mris_sphere ru_maxrss 411804 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 688263 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 18192 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 101394 mris_sphere ru_nivcsw 360 FSRUNTIME@ mris_sphere 0.0383 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy rh Tue May 25 21:02:47 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology rh Tue May 25 21:02:47 UTC 2021 mris_fix_topology -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-03 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-82 (nv=258622, nf=517408, ne=776112, g=42) 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 11 iterations marking ambiguous vertices... 9333 ambiguous faces found in tessellation segmenting defects... 62 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 44 into 47 -merging segment 55 into 54 60 defects to be corrected 0 vertices coincident reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5000 (-4.7500) -vertex loglikelihood: -5.9769 (-2.9885) -normal dot loglikelihood: -3.5352 (-3.5352) -quad curv loglikelihood: -6.3469 (-3.1735) Total Loglikelihood : -25.3591 CORRECTING DEFECT 0 (vertices=100, convex hull=31, v0=614) After retessellation of defect 0 (v0=614), euler #=-56 (253081,757591,504454) : difference with theory (-57) = -1 CORRECTING DEFECT 1 (vertices=549, convex hull=288, v0=885) After retessellation of defect 1 (v0=885), euler #=-55 (253144,757920,504721) : difference with theory (-56) = -1 CORRECTING DEFECT 2 (vertices=62, convex hull=86, v0=1412) After retessellation of defect 2 (v0=1412), euler #=-54 (253160,758000,504786) : difference with theory (-55) = -1 CORRECTING DEFECT 3 (vertices=18, convex hull=27, v0=2336) After retessellation of defect 3 (v0=2336), euler #=-53 (253161,758014,504800) : difference with theory (-54) = -1 CORRECTING DEFECT 4 (vertices=59, convex hull=40, v0=12568) After retessellation of defect 4 (v0=12568), euler #=-52 (253163,758033,504818) : difference with theory (-53) = -1 CORRECTING DEFECT 5 (vertices=692, convex hull=340, v0=14637) After retessellation of defect 5 (v0=14637), euler #=-51 (253238,758424,505135) : difference with theory (-52) = -1 CORRECTING DEFECT 6 (vertices=51, convex hull=79, v0=16819) After retessellation of defect 6 (v0=16819), euler #=-50 (253247,758482,505185) : difference with theory (-51) = -1 CORRECTING DEFECT 7 (vertices=32, convex hull=28, v0=21738) After retessellation of defect 7 (v0=21738), euler #=-49 (253248,758492,505195) : difference with theory (-50) = -1 CORRECTING DEFECT 8 (vertices=29, convex hull=14, v0=36316) After retessellation of defect 8 (v0=36316), euler #=-48 (253249,758501,505204) : difference with theory (-49) = -1 CORRECTING DEFECT 9 (vertices=6, convex hull=11, v0=40969) After retessellation of defect 9 (v0=40969), euler #=-47 (253250,758508,505211) : difference with theory (-48) = -1 CORRECTING DEFECT 10 (vertices=21, convex hull=24, v0=45163) After retessellation of defect 10 (v0=45163), euler #=-46 (253252,758521,505223) : difference with theory (-47) = -1 CORRECTING DEFECT 11 (vertices=39, convex hull=30, v0=50610) After retessellation of defect 11 (v0=50610), euler #=-45 (253256,758540,505239) : difference with theory (-46) = -1 CORRECTING DEFECT 12 (vertices=52, convex hull=77, v0=54191) After retessellation of defect 12 (v0=54191), euler #=-44 (253265,758598,505289) : difference with theory (-45) = -1 CORRECTING DEFECT 13 (vertices=44, convex hull=34, v0=69760) After retessellation of defect 13 (v0=69760), euler #=-43 (253267,758614,505304) : difference with theory (-44) = -1 CORRECTING DEFECT 14 (vertices=24, convex hull=27, v0=84018) After retessellation of defect 14 (v0=84018), euler #=-42 (253270,758631,505319) : difference with theory (-43) = -1 CORRECTING DEFECT 15 (vertices=47, convex hull=28, v0=91257) After retessellation of defect 15 (v0=91257), euler #=-41 (253274,758654,505339) : difference with theory (-42) = -1 CORRECTING DEFECT 16 (vertices=28, convex hull=47, v0=93332) After retessellation of defect 16 (v0=93332), euler #=-40 (253279,758688,505369) : difference with theory (-41) = -1 CORRECTING DEFECT 17 (vertices=8, convex hull=31, v0=96084) After retessellation of defect 17 (v0=96084), euler #=-39 (253283,758708,505386) : difference with theory (-40) = -1 CORRECTING DEFECT 18 (vertices=44, convex hull=59, v0=96241) After retessellation of defect 18 (v0=96241), euler #=-38 (253293,758762,505431) : difference with theory (-39) = -1 CORRECTING DEFECT 19 (vertices=920, convex hull=509, v0=97730) After retessellation of defect 19 (v0=97730), euler #=-37 (253308,759076,505731) : difference with theory (-38) = -1 CORRECTING DEFECT 20 (vertices=29, convex hull=34, v0=115163) After retessellation of defect 20 (v0=115163), euler #=-36 (253311,759093,505746) : difference with theory (-37) = -1 CORRECTING DEFECT 21 (vertices=127, convex hull=97, v0=118833) After retessellation of defect 21 (v0=118833), euler #=-35 (253339,759218,505844) : difference with theory (-36) = -1 CORRECTING DEFECT 22 (vertices=67, convex hull=45, v0=120304) After retessellation of defect 22 (v0=120304), euler #=-36 (253347,759268,505885) : difference with theory (-35) = 1 CORRECTING DEFECT 23 (vertices=57, convex hull=48, v0=120723) After retessellation of defect 23 (v0=120723), euler #=-35 (253352,759299,505912) : difference with theory (-34) = 1 CORRECTING DEFECT 24 (vertices=29, convex hull=53, v0=121181) After retessellation of defect 24 (v0=121181), euler #=-34 (253357,759336,505945) : difference with theory (-33) = 1 CORRECTING DEFECT 25 (vertices=54, convex hull=65, v0=122949) After retessellation of defect 25 (v0=122949), euler #=-33 (253365,759390,505992) : difference with theory (-32) = 1 CORRECTING DEFECT 26 (vertices=58, convex hull=41, v0=138261) After retessellation of defect 26 (v0=138261), euler #=-32 (253372,759426,506022) : difference with theory (-31) = 1 CORRECTING DEFECT 27 (vertices=5, convex hull=21, v0=138298) After retessellation of defect 27 (v0=138298), euler #=-31 (253373,759434,506030) : difference with theory (-30) = 1 CORRECTING DEFECT 28 (vertices=23, convex hull=25, v0=143472) After retessellation of defect 28 (v0=143472), euler #=-30 (253374,759443,506039) : difference with theory (-29) = 1 CORRECTING DEFECT 29 (vertices=123, convex hull=29, v0=144540) After retessellation of defect 29 (v0=144540), euler #=-29 (253379,759464,506056) : difference with theory (-28) = 1 CORRECTING DEFECT 30 (vertices=26, convex hull=31, v0=149457) After retessellation of defect 30 (v0=149457), euler #=-28 (253381,759481,506072) : difference with theory (-27) = 1 CORRECTING DEFECT 31 (vertices=75, convex hull=37, v0=150966) After retessellation of defect 31 (v0=150966), euler #=-27 (253387,759512,506098) : difference with theory (-26) = 1 CORRECTING DEFECT 32 (vertices=36, convex hull=45, v0=151495) After retessellation of defect 32 (v0=151495), euler #=-26 (253395,759552,506131) : difference with theory (-25) = 1 CORRECTING DEFECT 33 (vertices=17, convex hull=52, v0=152017) After retessellation of defect 33 (v0=152017), euler #=-25 (253400,759587,506162) : difference with theory (-24) = 1 CORRECTING DEFECT 34 (vertices=12, convex hull=18, v0=152690) After retessellation of defect 34 (v0=152690), euler #=-24 (253402,759595,506169) : difference with theory (-23) = 1 CORRECTING DEFECT 35 (vertices=255, convex hull=50, v0=152734) After retessellation of defect 35 (v0=152734), euler #=-23 (253414,759666,506229) : difference with theory (-22) = 1 CORRECTING DEFECT 36 (vertices=41, convex hull=32, v0=161996) After retessellation of defect 36 (v0=161996), euler #=-22 (253417,759683,506244) : difference with theory (-21) = 1 CORRECTING DEFECT 37 (vertices=63, convex hull=25, v0=164311) After retessellation of defect 37 (v0=164311), euler #=-21 (253426,759718,506271) : difference with theory (-20) = 1 CORRECTING DEFECT 38 (vertices=113, convex hull=53, v0=167312) After retessellation of defect 38 (v0=167312), euler #=-20 (253434,759765,506311) : difference with theory (-19) = 1 CORRECTING DEFECT 39 (vertices=57, convex hull=29, v0=170628) After retessellation of defect 39 (v0=170628), euler #=-19 (253438,759786,506329) : difference with theory (-18) = 1 CORRECTING DEFECT 40 (vertices=8, convex hull=15, v0=171208) After retessellation of defect 40 (v0=171208), euler #=-18 (253438,759790,506334) : difference with theory (-17) = 1 CORRECTING DEFECT 41 (vertices=396, convex hull=237, v0=171986) After retessellation of defect 41 (v0=171986), euler #=-18 (253529,760181,506634) : difference with theory (-16) = 2 CORRECTING DEFECT 42 (vertices=192, convex hull=54, v0=173715) After retessellation of defect 42 (v0=173715), euler #=-17 (253536,760224,506671) : difference with theory (-15) = 2 CORRECTING DEFECT 43 (vertices=54, convex hull=54, v0=176230) After retessellation of defect 43 (v0=176230), euler #=-16 (253546,760276,506714) : difference with theory (-14) = 2 CORRECTING DEFECT 44 (vertices=154, convex hull=40, v0=177640) After retessellation of defect 44 (v0=177640), euler #=-15 (253555,760315,506745) : difference with theory (-13) = 2 CORRECTING DEFECT 45 (vertices=75, convex hull=41, v0=180761) After retessellation of defect 45 (v0=180761), euler #=-14 (253560,760346,506772) : difference with theory (-12) = 2 CORRECTING DEFECT 46 (vertices=49, convex hull=28, v0=180917) After retessellation of defect 46 (v0=180917), euler #=-12 (253564,760367,506791) : difference with theory (-11) = 1 CORRECTING DEFECT 47 (vertices=112, convex hull=106, v0=184110) After retessellation of defect 47 (v0=184110), euler #=-11 (253575,760455,506869) : difference with theory (-10) = 1 CORRECTING DEFECT 48 (vertices=25, convex hull=56, v0=185910) After retessellation of defect 48 (v0=185910), euler #=-10 (253584,760503,506909) : difference with theory (-9) = 1 CORRECTING DEFECT 49 (vertices=31, convex hull=64, v0=187788) After retessellation of defect 49 (v0=187788), euler #=-9 (253592,760553,506952) : difference with theory (-8) = 1 CORRECTING DEFECT 50 (vertices=30, convex hull=62, v0=196856) After retessellation of defect 50 (v0=196856), euler #=-8 (253601,760603,506994) : difference with theory (-7) = 1 CORRECTING DEFECT 51 (vertices=42, convex hull=14, v0=198298) After retessellation of defect 51 (v0=198298), euler #=-7 (253601,760605,506997) : difference with theory (-6) = 1 CORRECTING DEFECT 52 (vertices=11, convex hull=28, v0=200483) After retessellation of defect 52 (v0=200483), euler #=-6 (253603,760622,507013) : difference with theory (-5) = 1 CORRECTING DEFECT 53 (vertices=111, convex hull=104, v0=203044) After retessellation of defect 53 (v0=203044), euler #=-4 (253617,760714,507093) : difference with theory (-4) = 0 CORRECTING DEFECT 54 (vertices=21, convex hull=61, v0=206168) After retessellation of defect 54 (v0=206168), euler #=-3 (253624,760756,507129) : difference with theory (-3) = 0 CORRECTING DEFECT 55 (vertices=14, convex hull=20, v0=219295) After retessellation of defect 55 (v0=219295), euler #=-2 (253626,760768,507140) : difference with theory (-2) = 0 CORRECTING DEFECT 56 (vertices=16, convex hull=44, v0=226099) After retessellation of defect 56 (v0=226099), euler #=-1 (253630,760796,507165) : difference with theory (-1) = 0 CORRECTING DEFECT 57 (vertices=7, convex hull=32, v0=234992) After retessellation of defect 57 (v0=234992), euler #=0 (253631,760807,507176) : difference with theory (0) = 0 CORRECTING DEFECT 58 (vertices=54, convex hull=96, v0=241580) After retessellation of defect 58 (v0=241580), euler #=1 (253640,760877,507238) : difference with theory (1) = 0 CORRECTING DEFECT 59 (vertices=42, convex hull=79, v0=248009) After retessellation of defect 59 (v0=248009), euler #=2 (253649,760941,507294) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.71 +- 0.19 (0.05-->13.06) (max @ vno 106110 --> 114387) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.71 +- 0.19 (0.05-->13.06) (max @ vno 106110 --> 114387) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 248 mutations (37.6%), 411 crossovers (62.4%), 196 vertices were eliminated building final representation... 4973 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=253649, nf=507294, ne=760941, g=0) writing corrected surface to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 34.0 minutes 0 defective edges removing intersecting faces 000: 462 intersecting 001: 7 intersecting mris_fix_topology utimesec 2051.211333 mris_fix_topology stimesec 0.617551 mris_fix_topology ru_maxrss 810564 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 412592 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 23912 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5238 mris_fix_topology ru_nivcsw 554 FSRUNTIME@ mris_fix_topology rh 0.5670 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 253649 - 760941 + 507294 = 2 --> 0 holes F =2V-4: 507294 = 507298-4 (0) 2E=3F: 1521882 = 1521882 (0) total defect index = 0 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 84 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue May 25 21:36:57 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-03 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... 48538 bright wm thresholded. 856 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.orig... computing class statistics... border white: 523483 voxels (1.60%) border gray 522637 voxels (1.59%) WM (103.0): 103.0 +- 6.3 [70.0 --> 110.0] GM (83.0) : 82.3 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.3 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.67 +- 0.18 (0.01-->5.32) (max @ vno 106110 --> 109323) face area 0.19 +- 0.08 (0.00-->6.32) mean absolute distance = 1.44 +- 1.54 8186 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+-2.6, GM=78+-7.8 mean inside = 101.0, mean outside = 83.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=96.5, 126 (126) missing vertices, mean dist -0.8 [2.0 (%54.3)->0.6 (%45.7))] %43 local maxima, %42 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.71 +- 0.20 (0.02-->4.85) (max @ vno 111173 --> 124770) face area 0.19 +- 0.09 (0.00-->5.66) mean absolute distance = 0.59 +- 0.78 7724 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5658432.5, rms=9.633 001: dt: 0.5000, sse=2808080.5, rms=5.935 (38.391%) 002: dt: 0.5000, sse=1861935.5, rms=3.920 (33.947%) 003: dt: 0.5000, sse=1615726.1, rms=3.278 (16.371%) 004: dt: 0.5000, sse=1564607.0, rms=3.089 (5.776%) 005: dt: 0.5000, sse=1537556.0, rms=3.021 (2.209%) rms = 2.98, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=1553538.6, rms=2.978 (1.428%) 007: dt: 0.2500, sse=1292271.0, rms=1.843 (38.090%) 008: dt: 0.2500, sse=1233799.4, rms=1.547 (16.082%) 009: dt: 0.2500, sse=1227843.4, rms=1.453 (6.089%) 010: dt: 0.2500, sse=1204051.1, rms=1.377 (5.234%) rms = 1.34, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=1199293.6, rms=1.340 (2.687%) rms = 1.31, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=1203314.6, rms=1.309 (2.313%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=95.5, 212 (37) missing vertices, mean dist -0.1 [0.9 (%39.1)->0.3 (%60.9))] %78 local maxima, %15 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg56, 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 0.69 +- 0.19 (0.03-->5.26) (max @ vno 111173 --> 124770) face area 0.21 +- 0.10 (0.00-->7.01) mean absolute distance = 0.33 +- 0.55 9336 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2086910.0, rms=4.182 013: dt: 0.5000, sse=1614294.4, rms=2.692 (35.617%) rms = 2.64, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=1565840.8, rms=2.644 (1.804%) 015: dt: 0.2500, sse=1377953.9, rms=1.421 (46.251%) 016: dt: 0.2500, sse=1285521.2, rms=1.132 (20.341%) 017: dt: 0.2500, sse=1281275.1, rms=1.052 (7.085%) rms = 1.01, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=1277349.8, rms=1.013 (3.659%) rms = 0.97, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=1277817.5, rms=0.969 (4.347%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=95.7, 198 (20) missing vertices, mean dist -0.1 [0.5 (%40.2)->0.2 (%59.8))] %89 local maxima, % 5 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg56, 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 0.69 +- 0.19 (0.02-->5.47) (max @ vno 111173 --> 124770) face area 0.20 +- 0.10 (0.00-->7.15) mean absolute distance = 0.23 +- 0.41 7416 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1458679.6, rms=2.302 020: dt: 0.5000, sse=1425003.5, rms=2.049 (10.982%) rms = 2.41, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=1265725.5, rms=1.331 (35.029%) 022: dt: 0.2500, sse=1247667.1, rms=1.027 (22.880%) 023: dt: 0.2500, sse=1247422.4, rms=0.965 (6.030%) rms = 0.95, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=1231085.9, rms=0.946 (1.987%) rms = 0.90, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=1239131.2, rms=0.898 (5.014%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=95.5, 204 (15) missing vertices, mean dist -0.0 [0.4 (%33.9)->0.1 (%66.1))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg56, 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-03/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=1311023.4, rms=1.537 026: dt: 0.5000, sse=1307745.2, rms=1.468 (4.472%) rms = 1.96, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=1204936.0, rms=0.931 (36.605%) 028: dt: 0.2500, sse=1218014.9, rms=0.824 (11.472%) rms = 0.79, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=1208921.2, rms=0.788 (4.312%) rms = 0.75, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=1190498.4, rms=0.746 (5.347%) positioning took 0.7 minutes generating cortex label... 29 non-cortical segments detected only using segment with 10937 vertices erasing segment 0 (vno[0] = 88089) erasing segment 1 (vno[0] = 88093) erasing segment 3 (vno[0] = 109350) erasing segment 4 (vno[0] = 137387) erasing segment 5 (vno[0] = 168058) erasing segment 6 (vno[0] = 173481) erasing segment 7 (vno[0] = 176209) erasing segment 8 (vno[0] = 179212) erasing segment 9 (vno[0] = 179270) erasing segment 10 (vno[0] = 179293) erasing segment 11 (vno[0] = 179375) erasing segment 12 (vno[0] = 180841) erasing segment 13 (vno[0] = 180890) erasing segment 14 (vno[0] = 180941) erasing segment 15 (vno[0] = 182624) erasing segment 16 (vno[0] = 182679) erasing segment 17 (vno[0] = 183880) erasing segment 18 (vno[0] = 183890) erasing segment 19 (vno[0] = 184008) erasing segment 20 (vno[0] = 185066) erasing segment 21 (vno[0] = 186365) erasing segment 22 (vno[0] = 187588) erasing segment 23 (vno[0] = 187649) erasing segment 24 (vno[0] = 188901) erasing segment 25 (vno[0] = 190066) erasing segment 26 (vno[0] = 190123) erasing segment 27 (vno[0] = 217728) erasing segment 28 (vno[0] = 253561) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.area vertex spacing 0.69 +- 0.20 (0.01-->5.60) (max @ vno 111173 --> 124770) face area 0.20 +- 0.10 (0.00-->7.12) refinement took 5.7 minutes #-------------------------------------------- #@# Smooth2 rh Tue May 25 21:42:40 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue May 25 21:42:47 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_inflate -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_inflate.rh.dat -n 50 ../surf/rh.smoothwm ../surf/rh.inflated niterations = 50 Reading ../surf/rh.smoothwm avg radius = 48.0 mm, total surface area = 94157 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.154 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) step 065: RMS=0.020 (target=0.015) step 070: RMS=0.019 (target=0.015) step 075: RMS=0.018 (target=0.015) step 080: RMS=0.017 (target=0.015) step 085: RMS=0.017 (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 0.7 minutes mris_inflate utimesec 207.436425 mris_inflate stimesec 1.807581 mris_inflate ru_maxrss 403912 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 692380 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 19824 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 89842 mris_inflate ru_nivcsw 79 #-------------------------------------------- #@# Curv .H and .K rh Tue May 25 21:43:27 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf mris_curvature -w rh.white.preaparc total integrated curvature = 49.997*4pi (628.277) --> -49 handles ICI = 285.1, FI = 3110.3, variation=47817.532 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 463 vertices thresholded to be in k1 ~ [-0.19 0.31], k2 ~ [-0.09 0.05] total integrated curvature = 0.597*4pi (7.498) --> 0 handles ICI = 1.5, FI = 9.2, variation=157.363 256 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 312 vertices thresholded to be in [-0.12 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.021 done. #----------------------------------------- #@# Curvature Stats rh Tue May 25 21:45:01 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-03 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-03/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 472 ] Gb_filter = 0 WARN: S lookup min: -0.406222 WARN: S explicit min: 0.000000 vertex = 1006 #-------------------------------------------- #@# Sphere rh Tue May 25 21:45:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_sphere -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.268... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=blg56, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.86 pass 1: epoch 2 of 3 starting distance error %21.77 unfolding complete - removing small folds... starting distance error %21.65 removing remaining folds... final distance error %21.66 MRISunfold() return, current seed 1234 -01: dt=0.0000, 346 negative triangles 131: dt=0.9900, 346 negative triangles 132: dt=0.9900, 186 negative triangles 133: dt=0.9900, 157 negative triangles 134: dt=0.9900, 136 negative triangles 135: dt=0.9900, 133 negative triangles 136: dt=0.9900, 94 negative triangles 137: dt=0.9900, 101 negative triangles 138: dt=0.9900, 104 negative triangles 139: dt=0.9900, 84 negative triangles 140: dt=0.9900, 85 negative triangles 141: dt=0.9900, 71 negative triangles 142: dt=0.9900, 72 negative triangles 143: dt=0.9900, 67 negative triangles 144: dt=0.9900, 75 negative triangles 145: dt=0.9900, 59 negative triangles 146: dt=0.9900, 51 negative triangles 147: dt=0.9900, 48 negative triangles 148: dt=0.9900, 51 negative triangles 149: dt=0.9900, 57 negative triangles 150: dt=0.9900, 47 negative triangles 151: dt=0.9900, 44 negative triangles 152: dt=0.9900, 32 negative triangles 153: dt=0.9900, 41 negative triangles 154: dt=0.9900, 30 negative triangles 155: dt=0.9900, 32 negative triangles 156: dt=0.9900, 30 negative triangles 157: dt=0.9900, 30 negative triangles 158: dt=0.9900, 18 negative triangles 159: dt=0.9900, 29 negative triangles 160: dt=0.9900, 16 negative triangles 161: dt=0.9900, 22 negative triangles 162: dt=0.9900, 17 negative triangles 163: dt=0.9900, 18 negative triangles 164: dt=0.9900, 16 negative triangles 165: dt=0.9900, 11 negative triangles 166: dt=0.9900, 14 negative triangles 167: dt=0.9900, 8 negative triangles 168: dt=0.9900, 7 negative triangles 169: dt=0.9900, 4 negative triangles 170: dt=0.9900, 6 negative triangles 171: dt=0.9900, 9 negative triangles 172: dt=0.9900, 2 negative triangles 173: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.19 hours mris_sphere utimesec 4727.107949 mris_sphere stimesec 4.420468 mris_sphere ru_maxrss 558860 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 2493080 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 17848 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 119121 mris_sphere ru_nivcsw 2591 FSRUNTIME@ mris_sphere 0.1934 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Tue May 25 21:56:43 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts cmdline mris_register -curv -rusage /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=blg56, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=blg56, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.768 curvature mean = 0.023, std = 0.797 curvature mean = 0.023, std = 0.855 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 610419.2, tmin=1.2866 d=32.00 min @ (0.00, -8.00, -8.00) sse = 488707.9, tmin=2.5845 d=16.00 min @ (4.00, 4.00, 4.00) sse = 381061.6, tmin=3.8522 d=8.00 min @ (2.00, 0.00, 0.00) sse = 369330.8, tmin=5.1002 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 364357.4, tmin=6.3673 d=1.00 min @ (0.25, 0.00, 0.00) sse = 364150.1, tmin=8.9004 tol=1.0e+00, sigma=0.5, host=blg56, 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 10.16 min curvature mean = -0.008, std = 0.813 curvature mean = 0.008, std = 0.943 curvature mean = -0.015, std = 0.817 curvature mean = 0.003, std = 0.976 curvature mean = -0.018, std = 0.816 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.036, std = 0.370 curvature mean = 0.032, std = 0.235 curvature mean = 0.044, std = 0.281 curvature mean = 0.029, std = 0.289 curvature mean = 0.022, std = 0.442 curvature mean = 0.029, std = 0.315 curvature mean = 0.012, std = 0.573 curvature mean = 0.028, std = 0.327 curvature mean = 0.004, std = 0.678 MRISregister() return, current seed 0 -01: dt=0.0000, 131 negative triangles 122: dt=0.9900, 131 negative triangles 123: dt=0.9900, 127 negative triangles 124: dt=0.9900, 115 negative triangles 125: dt=0.9900, 125 negative triangles 126: dt=0.9900, 98 negative triangles 127: dt=0.9900, 87 negative triangles 128: dt=0.9900, 95 negative triangles 129: dt=0.9900, 83 negative triangles 130: dt=0.9900, 81 negative triangles 131: dt=0.9900, 72 negative triangles 132: dt=0.9900, 61 negative triangles 133: dt=0.9900, 62 negative triangles 134: dt=0.9900, 55 negative triangles 135: dt=0.9900, 51 negative triangles 136: dt=0.9900, 45 negative triangles 137: dt=0.9900, 44 negative triangles 138: dt=0.9900, 35 negative triangles 139: dt=0.9900, 41 negative triangles 140: dt=0.9900, 29 negative triangles 141: dt=0.9900, 27 negative triangles 142: dt=0.9900, 24 negative triangles 143: dt=0.9900, 21 negative triangles 144: dt=0.9900, 18 negative triangles 145: dt=0.9900, 21 negative triangles 146: dt=0.9900, 16 negative triangles 147: dt=0.9900, 20 negative triangles 148: dt=0.9900, 10 negative triangles 149: dt=0.9900, 16 negative triangles 150: dt=0.9900, 8 negative triangles 151: dt=0.9900, 11 negative triangles 152: dt=0.9900, 5 negative triangles 153: dt=0.9900, 9 negative triangles 154: dt=0.9900, 12 negative triangles 155: dt=0.9900, 11 negative triangles 156: dt=0.9900, 3 negative triangles 157: dt=0.9900, 7 negative triangles 158: dt=0.9900, 4 negative triangles 159: dt=0.9900, 2 negative triangles 160: dt=0.9900, 4 negative triangles 161: dt=0.9900, 1 negative triangles 162: dt=0.9900, 1 negative triangles 163: dt=0.9900, 3 negative triangles 164: dt=0.9900, 1 negative triangles 165: dt=0.9900, 1 negative triangles 166: dt=0.9900, 1 negative triangles 167: dt=0.9900, 3 negative triangles 168: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.52 hours mris_register utimesec 8299.075140 mris_register stimesec 5.728215 mris_register ru_maxrss 453828 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 3060165 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5582 mris_register ru_oublock 17848 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 130226 mris_register ru_nivcsw 4050 FSRUNTIME@ mris_register 0.5228 hours 1 threads #-------------------------------------------- #@# Jacobian white rh Tue May 25 22:28:05 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue May 25 22:28:07 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue May 25 22:28:09 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 2562 labels changed using aseg relabeling using gibbs priors... 000: 4546 changed, 253649 examined... 001: 1094 changed, 19112 examined... 002: 295 changed, 6020 examined... 003: 111 changed, 1755 examined... 004: 39 changed, 626 examined... 005: 19 changed, 218 examined... 006: 12 changed, 118 examined... 007: 3 changed, 66 examined... 008: 4 changed, 20 examined... 009: 1 changed, 17 examined... 010: 0 changed, 4 examined... 224 labels changed using aseg 000: 158 total segments, 120 labels (835 vertices) changed 001: 43 total segments, 5 labels (7 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 3200 vertices marked for relabeling... 3200 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 17 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue May 25 22:28:27 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-03 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/filled.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brain.finalsurfs.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/../mri/aseg.presurf.mgz... reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... 48538 bright wm thresholded. 856 bright non-wm voxels segmented. reading original surface position from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.orig... computing class statistics... border white: 523483 voxels (1.60%) border gray 522637 voxels (1.59%) WM (103.0): 103.0 +- 6.3 [70.0 --> 110.0] GM (83.0) : 82.3 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.3 (was 40) setting MAX_GRAY to 102.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40) spring scale = 1.25 using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=109+-2.6, GM=78+-7.8 mean inside = 101.0, mean outside = 83.6 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 0.69 +- 0.20 (0.01-->5.60) (max @ vno 111173 --> 124770) face area 0.20 +- 0.10 (0.00-->7.13) mean absolute distance = 1.29 +- 1.36 7335 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 90 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 48 points - only 0.00% unknown deleting segment 5 with 30 points - only 0.00% unknown deleting segment 6 with 113 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 156 points - only 0.00% unknown deleting segment 9 with 160 points - only 0.00% unknown deleting segment 10 with 107 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 158 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 9 points - only 0.00% unknown deleting segment 17 with 16 points - only 0.00% unknown deleting segment 18 with 145 points - only 0.00% unknown deleting segment 19 with 19 points - only 0.00% unknown mean border=96.4, 205 (180) missing vertices, mean dist -0.5 [2.2 (%40.3)->0.6 (%59.7))] %43 local maxima, %42 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.70 +- 0.19 (0.03-->5.81) (max @ vno 111173 --> 124770) face area 0.20 +- 0.10 (0.00-->7.39) mean absolute distance = 0.57 +- 0.77 7462 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2621250.5, rms=5.426 001: dt: 0.5000, sse=1635225.8, rms=3.041 (43.960%) 002: dt: 0.5000, sse=1536439.0, rms=2.677 (11.979%) rms = 2.71, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=1347781.1, rms=1.897 (29.142%) 004: dt: 0.2500, sse=1297760.4, rms=1.472 (22.398%) 005: dt: 0.2500, sse=1272743.5, rms=1.366 (7.161%) 006: dt: 0.2500, sse=1270681.8, rms=1.314 (3.802%) rms = 1.29, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=1288306.1, rms=1.294 (1.567%) rms = 1.27, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=1253861.8, rms=1.269 (1.937%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 100 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 36 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 26 points - only 0.00% unknown deleting segment 5 with 120 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown deleting segment 7 with 150 points - only 0.00% unknown deleting segment 8 with 80 points - only 0.00% unknown deleting segment 9 with 141 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 145 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 56 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 8 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown deleting segment 18 with 125 points - only 0.00% unknown deleting segment 19 with 19 points - only 0.00% unknown mean border=95.5, 216 (63) missing vertices, mean dist -0.1 [0.9 (%38.4)->0.3 (%61.6))] %79 local maxima, %14 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=blg56, 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 0.69 +- 0.19 (0.04-->5.94) (max @ vno 111173 --> 124770) face area 0.21 +- 0.10 (0.00-->7.58) mean absolute distance = 0.32 +- 0.55 9378 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2011889.1, rms=4.056 009: dt: 0.5000, sse=1556212.9, rms=2.628 (35.199%) rms = 2.63, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=1544453.4, rms=2.626 (0.096%) 011: dt: 0.2500, sse=1326159.6, rms=1.443 (45.021%) 012: dt: 0.2500, sse=1280831.5, rms=1.188 (17.679%) 013: dt: 0.2500, sse=1271635.4, rms=1.126 (5.204%) rms = 1.09, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=1274961.2, rms=1.089 (3.322%) rms = 1.05, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=1257550.9, rms=1.048 (3.725%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 102 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 33 points - only 0.00% unknown deleting segment 3 with 121 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 124 points - only 0.00% unknown deleting segment 6 with 98 points - only 0.00% unknown deleting segment 7 with 129 points - only 0.00% unknown deleting segment 8 with 148 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown deleting segment 10 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 43 points - only 0.00% unknown deleting segment 13 with 27 points - only 0.00% unknown deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown deleting segment 16 with 11 points - only 0.00% unknown deleting segment 17 with 128 points - only 0.00% unknown deleting segment 18 with 19 points - only 0.00% unknown mean border=95.7, 238 (38) missing vertices, mean dist -0.1 [0.5 (%40.1)->0.2 (%59.9))] %90 local maxima, % 5 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=blg56, 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 0.69 +- 0.19 (0.03-->6.02) (max @ vno 111173 --> 124770) face area 0.20 +- 0.10 (0.00-->7.39) mean absolute distance = 0.23 +- 0.41 7366 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1433680.6, rms=2.313 016: dt: 0.5000, sse=1405947.5, rms=2.082 (9.984%) rms = 2.42, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=1264173.5, rms=1.382 (33.661%) 018: dt: 0.2500, sse=1235071.5, rms=1.086 (21.360%) 019: dt: 0.2500, sse=1230310.8, rms=1.027 (5.445%) rms = 1.01, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=1248306.0, rms=1.009 (1.802%) rms = 0.97, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=1216500.5, rms=0.970 (3.888%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 104 points - only 0.00% unknown deleting segment 1 with 47 points - only 0.00% unknown deleting segment 2 with 27 points - only 0.00% unknown deleting segment 3 with 99 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 129 points - only 0.00% unknown deleting segment 6 with 88 points - only 0.00% unknown deleting segment 7 with 135 points - only 0.00% unknown deleting segment 8 with 176 points - only 0.00% unknown deleting segment 9 with 24 points - only 0.00% unknown deleting segment 11 with 18 points - only 0.00% unknown deleting segment 12 with 27 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 14 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 15 points - only 0.00% unknown deleting segment 17 with 128 points - only 0.00% unknown deleting segment 18 with 20 points - only 0.00% unknown mean border=95.5, 259 (27) missing vertices, mean dist -0.0 [0.4 (%33.7)->0.1 (%66.3))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=blg56, 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-03/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=1282232.4, rms=1.539 rms = 1.51, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=1285834.0, rms=1.509 (1.953%) 023: dt: 0.2500, sse=1219682.2, rms=1.027 (31.947%) 024: dt: 0.2500, sse=1212469.0, rms=0.909 (11.473%) rms = 0.93, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=1190746.0, rms=0.843 (7.232%) 026: dt: 0.1250, sse=1187053.0, rms=0.774 (8.226%) rms = 0.76, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=1190264.1, rms=0.764 (1.300%) positioning took 0.8 minutes generating cortex label... 28 non-cortical segments detected only using segment with 10895 vertices erasing segment 0 (vno[0] = 88093) erasing segment 1 (vno[0] = 88095) erasing segment 3 (vno[0] = 137378) erasing segment 4 (vno[0] = 149169) erasing segment 5 (vno[0] = 168058) erasing segment 6 (vno[0] = 173481) erasing segment 7 (vno[0] = 176209) erasing segment 8 (vno[0] = 179193) erasing segment 9 (vno[0] = 179269) erasing segment 10 (vno[0] = 180841) erasing segment 11 (vno[0] = 180890) erasing segment 12 (vno[0] = 180941) erasing segment 13 (vno[0] = 180943) erasing segment 14 (vno[0] = 182460) erasing segment 15 (vno[0] = 182624) erasing segment 16 (vno[0] = 182637) erasing segment 17 (vno[0] = 182679) erasing segment 18 (vno[0] = 183880) erasing segment 19 (vno[0] = 183890) erasing segment 20 (vno[0] = 185066) erasing segment 21 (vno[0] = 186365) erasing segment 22 (vno[0] = 187588) erasing segment 23 (vno[0] = 187649) erasing segment 24 (vno[0] = 188901) erasing segment 25 (vno[0] = 190066) erasing segment 26 (vno[0] = 190123) erasing segment 27 (vno[0] = 217728) writing cortex label to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label... writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.area vertex spacing 0.69 +- 0.20 (0.02-->6.05) (max @ vno 111173 --> 124770) face area 0.20 +- 0.10 (0.00-->7.13) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 45 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 32 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown deleting segment 6 with 41 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 9 with 146 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 245 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown deleting segment 13 with 241 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown deleting segment 15 with 31 points - only 0.00% unknown deleting segment 16 with 39 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown deleting segment 18 with 247 points - only 2.43% unknown deleting segment 19 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown deleting segment 21 with 136 points - only 0.00% unknown deleting segment 22 with 13 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=75.3, 196 (196) missing vertices, mean dist 0.7 [1.0 (%0.0)->1.1 (%100.0))] %14 local maxima, %47 large gradients and %35 min vals, 83 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=blg56, 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=23428052.0, rms=21.380 001: dt: 0.0500, sse=18561308.0, rms=18.902 (11.589%) 002: dt: 0.0500, sse=16004122.0, rms=17.460 (7.632%) 003: dt: 0.0500, sse=14344473.0, rms=16.456 (5.751%) 004: dt: 0.0500, sse=13139552.0, rms=15.686 (4.676%) 005: dt: 0.0500, sse=12198821.0, rms=15.058 (4.005%) 006: dt: 0.0500, sse=11424170.0, rms=14.520 (3.571%) 007: dt: 0.0500, sse=10763565.0, rms=14.045 (3.271%) 008: dt: 0.0500, sse=10184304.0, rms=13.615 (3.063%) 009: dt: 0.0500, sse=9667342.0, rms=13.219 (2.908%) 010: dt: 0.0500, sse=9199016.0, rms=12.850 (2.794%) positioning took 1.2 minutes mean border=69.2, 137 (87) missing vertices, mean dist 0.8 [0.9 (%0.0)->1.3 (%100.0))] %15 local maxima, %47 large gradients and %35 min vals, 201 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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=19184378.0, rms=19.233 011: dt: 0.0500, sse=18480422.0, rms=18.853 (1.975%) 012: dt: 0.0500, sse=17848882.0, rms=18.505 (1.843%) 013: dt: 0.0500, sse=17275006.0, rms=18.184 (1.738%) 014: dt: 0.0500, sse=16749080.0, rms=17.884 (1.649%) 015: dt: 0.0500, sse=16264001.0, rms=17.603 (1.573%) 016: dt: 0.0500, sse=15812117.0, rms=17.336 (1.512%) 017: dt: 0.0500, sse=15387786.0, rms=17.082 (1.464%) 018: dt: 0.0500, sse=14982789.0, rms=16.837 (1.439%) 019: dt: 0.0500, sse=14590337.0, rms=16.595 (1.436%) 020: dt: 0.0500, sse=14206483.0, rms=16.355 (1.445%) positioning took 1.2 minutes mean border=67.7, 143 (59) missing vertices, mean dist 0.8 [0.2 (%0.2)->1.2 (%99.8))] %15 local maxima, %47 large gradients and %34 min vals, 208 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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=15678836.0, rms=17.259 021: dt: 0.0500, sse=15231920.0, rms=16.990 (1.558%) 022: dt: 0.0500, sse=14806510.0, rms=16.730 (1.531%) 023: dt: 0.0500, sse=14398984.0, rms=16.477 (1.513%) 024: dt: 0.0500, sse=14006443.0, rms=16.229 (1.503%) 025: dt: 0.0500, sse=13627514.0, rms=15.987 (1.495%) 026: dt: 0.0500, sse=13258038.0, rms=15.746 (1.503%) 027: dt: 0.0500, sse=12896159.0, rms=15.507 (1.518%) 028: dt: 0.0500, sse=12540161.0, rms=15.268 (1.540%) 029: dt: 0.0500, sse=12188245.0, rms=15.029 (1.571%) 030: dt: 0.0500, sse=11840784.0, rms=14.788 (1.601%) positioning took 1.2 minutes mean border=66.9, 171 (48) missing vertices, mean dist 0.6 [0.1 (%2.2)->1.0 (%97.8))] %15 local maxima, %47 large gradients and %34 min vals, 218 gradients ignored tol=1.0e-04, sigma=2.0, host=blg56, 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=12620909.0, rms=15.318 031: dt: 0.5000, sse=10169581.0, rms=13.566 (11.441%) 032: dt: 0.5000, sse=8055013.5, rms=11.850 (12.649%) 033: dt: 0.5000, sse=6337557.5, rms=10.259 (13.426%) 034: dt: 0.5000, sse=4901461.5, rms=8.700 (15.196%) 035: dt: 0.5000, sse=3936871.8, rms=7.481 (14.013%) 036: dt: 0.5000, sse=3290076.2, rms=6.533 (12.672%) 037: dt: 0.5000, sse=3024148.0, rms=6.107 (6.524%) 038: dt: 0.5000, sse=2848184.2, rms=5.802 (4.988%) 039: dt: 0.5000, sse=2815895.0, rms=5.748 (0.938%) 040: dt: 0.5000, sse=2742146.0, rms=5.612 (2.365%) rms = 5.63, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=2338248.0, rms=4.768 (15.031%) rms = 4.72, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=2325568.8, rms=4.723 (0.947%) 043: dt: 0.1250, sse=2153201.0, rms=4.314 (8.665%) 044: dt: 0.1250, sse=2114573.8, rms=4.219 (2.197%) rms = 4.23, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=2119247.5, rms=4.228 (-0.221%) positioning took 2.5 minutes mean border=64.7, 4494 (25) missing vertices, mean dist 0.2 [0.2 (%22.3)->0.4 (%77.7))] %33 local maxima, %30 large gradients and %32 min vals, 120 gradients ignored tol=1.0e-04, sigma=1.0, host=blg56, 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=3342458.2, rms=6.082 rms = 6.38, time step reduction 1 of 3 to 0.250... 046: dt: 0.2500, sse=3040831.2, rms=5.523 (9.182%) 047: dt: 0.2500, sse=2842573.2, rms=5.099 (7.687%) 048: dt: 0.2500, sse=2743524.0, rms=4.887 (4.153%) 049: dt: 0.2500, sse=2614125.0, rms=4.601 (5.844%) 050: dt: 0.2500, sse=2542494.8, rms=4.436 (3.588%) 051: dt: 0.2500, sse=2426853.2, rms=4.156 (6.326%) 052: dt: 0.2500, sse=2364724.2, rms=3.997 (3.822%) 053: dt: 0.2500, sse=2280388.8, rms=3.772 (5.630%) 054: dt: 0.2500, sse=2248922.5, rms=3.684 (2.338%) 055: dt: 0.2500, sse=2207486.8, rms=3.566 (3.184%) rms = 3.55, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=2200924.0, rms=3.548 (0.526%) 057: dt: 0.1250, sse=1909392.9, rms=2.510 (29.245%) 058: dt: 0.1250, sse=1865199.9, rms=2.324 (7.400%) rms = 2.30, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1860405.2, rms=2.304 (0.890%) positioning took 2.7 minutes mean border=63.5, 5124 (24) missing vertices, mean dist 0.1 [0.2 (%23.8)->0.2 (%76.2))] %44 local maxima, %19 large gradients and %31 min vals, 123 gradients ignored tol=1.0e-04, sigma=0.5, host=blg56, 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=2087389.9, rms=3.095 rms = 4.79, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1954816.0, rms=2.596 (16.108%) rms = 2.67, time step reduction 2 of 3 to 0.125... 061: dt: 0.1250, sse=1938095.5, rms=2.526 (2.729%) 062: dt: 0.1250, sse=1913233.4, rms=2.415 (4.388%) rms = 2.40, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1909857.8, rms=2.398 (0.699%) positioning took 1.0 minutes mean border=62.8, 9352 (21) missing vertices, mean dist 0.0 [0.2 (%28.9)->0.1 (%71.1))] %46 local maxima, %17 large gradients and %30 min vals, 117 gradients ignored tol=1.0e-04, sigma=0.2, host=blg56, 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-03/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1963627.0, rms=2.625 rms = 3.83, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1914693.0, rms=2.416 (7.978%) rms = 2.55, time step reduction 2 of 3 to 0.125... rms = 2.37, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1904768.9, rms=2.372 (1.802%) positioning took 0.6 minutes writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.area.pial vertex spacing 0.79 +- 0.34 (0.04-->6.97) (max @ vno 169536 --> 169506) face area 0.25 +- 0.20 (0.00-->7.13) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 253649 vertices processed 25000 of 253649 vertices processed 50000 of 253649 vertices processed 75000 of 253649 vertices processed 100000 of 253649 vertices processed 125000 of 253649 vertices processed 150000 of 253649 vertices processed 175000 of 253649 vertices processed 200000 of 253649 vertices processed 225000 of 253649 vertices processed 250000 of 253649 vertices processed 0 of 253649 vertices processed 25000 of 253649 vertices processed 50000 of 253649 vertices processed 75000 of 253649 vertices processed 100000 of 253649 vertices processed 125000 of 253649 vertices processed 150000 of 253649 vertices processed 175000 of 253649 vertices processed 200000 of 253649 vertices processed 225000 of 253649 vertices processed 250000 of 253649 vertices processed thickness calculation complete, 37:280 truncations. 52781 vertices at 0 distance 164095 vertices at 1 distance 155205 vertices at 2 distance 76823 vertices at 3 distance 27052 vertices at 4 distance 8063 vertices at 5 distance 2332 vertices at 6 distance 737 vertices at 7 distance 246 vertices at 8 distance 96 vertices at 9 distance 62 vertices at 10 distance 51 vertices at 11 distance 41 vertices at 12 distance 24 vertices at 13 distance 16 vertices at 14 distance 15 vertices at 15 distance 12 vertices at 16 distance 14 vertices at 17 distance 11 vertices at 18 distance 14 vertices at 19 distance 20 vertices at 20 distance writing curvature file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.thickness positioning took 17.8 minutes #-------------------------------------------- #@# Surf Volume rh Tue May 25 22:46:17 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-03 rh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.volume masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Total face volume 263980 Total vertex volume 261682 (mask=0) #@# sub-03 rh 261682 vertexvol Done #----------------------------------------- #@# Cortical Parc 2 rh Tue May 25 22:46:21 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 13 labels changed using aseg relabeling using gibbs priors... 000: 14559 changed, 253649 examined... 001: 3503 changed, 57326 examined... 002: 1088 changed, 18251 examined... 003: 432 changed, 6078 examined... 004: 229 changed, 2464 examined... 005: 122 changed, 1261 examined... 006: 54 changed, 675 examined... 007: 25 changed, 307 examined... 008: 13 changed, 129 examined... 009: 11 changed, 81 examined... 010: 5 changed, 54 examined... 011: 2 changed, 31 examined... 012: 1 changed, 13 examined... 013: 1 changed, 7 examined... 014: 0 changed, 7 examined... 0 labels changed using aseg 000: 411 total segments, 323 labels (5378 vertices) changed 001: 116 total segments, 29 labels (325 vertices) changed 002: 88 total segments, 1 labels (9 vertices) changed 003: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 64 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2439 vertices marked for relabeling... 2439 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Tue May 25 22:46:42 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 2142 labels changed using aseg relabeling using gibbs priors... 000: 3219 changed, 253649 examined... 001: 765 changed, 14810 examined... 002: 233 changed, 4362 examined... 003: 83 changed, 1372 examined... 004: 42 changed, 523 examined... 005: 16 changed, 250 examined... 006: 10 changed, 105 examined... 007: 6 changed, 53 examined... 008: 7 changed, 36 examined... 009: 3 changed, 35 examined... 010: 3 changed, 21 examined... 011: 2 changed, 15 examined... 012: 0 changed, 14 examined... 96 labels changed using aseg 000: 70 total segments, 37 labels (266 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2140 vertices marked for relabeling... 2140 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# WM/GM Contrast rh Tue May 25 22:46:59 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts pctsurfcon --s sub-03 --rh-only Log file is /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts/pctsurfcon.log Tue May 25 22:47:00 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-03/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux blg5611.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-03/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128249/rh.wm.mgh --regheader sub-03 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00002; 0.00000 0.00000 1.00000 0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 133684 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128249/rh.wm.mgh Dim: 253649 1 1 mri_vol2surf --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128249/rh.gm.mgh --projfrac 0.3 --regheader sub-03 --cortex srcvol = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00002; 0.00000 0.00000 1.00000 0.00001; 0.00000 -1.00000 0.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Reading surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Done reading source surface Reading thickness /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 159112 Masking with /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.cortex.label Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128249/rh.gm.mgh Dim: 253649 1 1 mri_concat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128249/rh.wm.mgh /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/tmp.pctsurfcon.128249/rh.gm.mgh --paired-diff-norm --mul 100 --o /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.w-g.pct.mgh mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.w-g.pct.mgh --annot sub-03 rh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.w-g.pct.mgh --annot sub-03 rh aparc --sum /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/stats/rh.w-g.pct.stats --snr sysname Linux hostname blg5611.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-03/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.w-g.pct.mgh Vertex Area is 0.400903 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up Started at Tue May 25 20:58:31 UTC 2021 Ended at Tue May 25 22:47:15 UTC 2021 #@#%# recon-all-run-time-hours 1.812 recon-all -s sub-03 finished without error at Tue May 25 22:47:16 UTC 2021 New invocation of recon-all Wed May 26 00:09:15 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-03 -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-03 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 blg5611.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 67108864 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 767933 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196638432 31834544 159002424 1957252 5801464 160445396 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.int.ets1.calculquebec.ca Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/05/26-00:09:15-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: blg5611.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 rh Wed May 26 00:09:16 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-03 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287397 Total vertex volume 284830 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2826 1219 3111 2.632 0.419 0.070 0.014 15 1.8 bankssts 2619 1050 3275 2.467 0.866 0.094 0.022 37 2.2 caudalanteriorcingulate 5339 2244 6883 2.781 0.439 0.085 0.024 47 6.3 caudalmiddlefrontal 4685 1747 4119 2.102 0.501 0.102 0.029 56 6.1 cuneus 1134 483 2249 3.292 0.628 0.083 0.029 9 1.3 entorhinal 8544 3449 12024 2.788 0.613 0.090 0.026 100 9.5 fusiform 15885 5993 17679 2.606 0.497 0.084 0.022 176 14.7 inferiorparietal 8725 3484 10941 2.637 0.625 0.086 0.027 96 11.0 inferiortemporal 3084 1261 3358 2.123 0.998 0.094 0.029 42 3.5 isthmuscingulate 15025 5713 13134 2.098 0.561 0.093 0.026 147 17.1 lateraloccipital 6983 2922 9219 2.656 0.518 0.095 0.027 88 8.1 lateralorbitofrontal 7519 3001 7027 2.048 0.644 0.099 0.029 89 9.2 lingual 5187 2124 6311 2.505 0.556 0.100 0.030 111 6.9 medialorbitofrontal 9569 3711 12367 2.752 0.682 0.076 0.021 88 8.2 middletemporal 1520 622 1893 2.730 0.820 0.061 0.012 7 0.7 parahippocampal 4443 1752 5195 2.603 0.466 0.084 0.022 38 4.5 paracentral 3193 1330 4599 2.866 0.501 0.092 0.022 34 3.0 parsopercularis 1866 757 2850 2.865 0.556 0.093 0.022 27 1.5 parsorbitalis 2828 1179 3725 2.751 0.475 0.088 0.021 28 2.6 parstriangularis 5018 1900 3616 2.022 0.585 0.096 0.035 62 7.5 pericalcarine 11567 4436 11016 2.233 0.453 0.076 0.019 90 9.6 postcentral 3115 1301 3802 2.430 0.808 0.095 0.022 39 2.9 posteriorcingulate 13860 4980 15311 2.753 0.495 0.068 0.021 119 11.9 precentral 11586 4835 13665 2.560 0.447 0.088 0.022 121 11.2 precuneus 1872 762 2766 2.760 0.752 0.098 0.026 29 1.9 rostralanteriorcingulate 19325 8181 23319 2.453 0.451 0.094 0.025 251 21.1 rostralmiddlefrontal 19518 8148 27063 2.802 0.582 0.093 0.024 223 21.0 superiorfrontal 14709 5924 15346 2.326 0.432 0.086 0.021 147 13.5 superiorparietal 9779 3902 13041 2.869 0.686 0.075 0.019 75 8.4 superiortemporal 10954 4032 11552 2.612 0.502 0.083 0.028 113 14.2 supramarginal 952 385 1554 2.713 0.544 0.125 0.036 23 1.6 frontalpole 1395 559 3219 3.760 0.757 0.109 0.046 19 2.9 temporalpole 1086 381 1314 2.699 0.370 0.082 0.019 9 0.9 transversetemporal 6475 2792 8250 2.707 0.922 0.106 0.054 104 17.4 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-03 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287397 Total vertex volume 284830 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2826 1120 3111 2.632 0.419 0.073 0.020 22 2.3 bankssts 2619 1391 3275 2.467 0.866 0.078 0.020 21 1.5 caudalanteriorcingulate 5339 2561 6883 2.781 0.439 0.074 0.021 68 5.1 caudalmiddlefrontal 4685 2124 4119 2.102 0.501 0.080 0.020 42 4.1 cuneus 1134 835 2249 3.292 0.628 0.097 0.017 5 1.0 entorhinal 8544 4628 12024 2.788 0.613 0.083 0.018 79 6.1 fusiform 15885 7376 17679 2.606 0.497 0.081 0.020 172 13.8 inferiorparietal 8725 4495 10941 2.637 0.625 0.079 0.019 136 6.3 inferiortemporal 3084 1680 3358 2.123 0.998 0.132 0.039 19186 4.1 isthmuscingulate 15025 6584 13134 2.098 0.561 0.072 0.018 142 11.0 lateraloccipital 6983 3688 9219 2.656 0.518 0.088 0.021 145 5.9 lateralorbitofrontal 7519 3623 7027 2.048 0.644 0.084 0.023 93 8.0 lingual 5187 2762 6311 2.505 0.556 0.088 0.023 52 4.4 medialorbitofrontal 9569 5071 12367 2.752 0.682 0.081 0.021 82 9.9 middletemporal 1520 741 1893 2.730 0.820 0.065 0.014 7 0.9 parahippocampal 4443 2093 5195 2.603 0.466 0.075 0.022 62 3.9 paracentral 3193 1755 4599 2.866 0.501 0.090 0.020 26 2.6 parsopercularis 1866 1164 2850 2.865 0.556 0.098 0.019 22 1.4 parsorbitalis 2828 1499 3725 2.751 0.475 0.094 0.021 33 2.7 parstriangularis 5018 1756 3616 2.022 0.585 0.071 0.035 142 6.6 pericalcarine 11567 5296 11016 2.233 0.453 0.074 0.016 73 7.8 postcentral 3115 1614 3802 2.430 0.808 0.085 0.026 108 2.2 posteriorcingulate 13860 5817 15311 2.753 0.495 0.064 0.015 106 8.7 precentral 11586 5444 13665 2.560 0.447 0.082 0.021 128 9.9 precuneus 1872 1142 2766 2.760 0.752 0.099 0.024 33 1.8 rostralanteriorcingulate 19325 10184 23319 2.453 0.451 0.092 0.022 240 18.0 rostralmiddlefrontal 19518 10205 27063 2.802 0.582 0.083 0.019 218 14.5 superiorfrontal 14709 6877 15346 2.326 0.432 0.079 0.018 156 10.5 superiorparietal 9779 4902 13041 2.869 0.686 0.082 0.019 83 8.5 superiortemporal 10954 4630 11552 2.612 0.502 0.078 0.028 131 16.0 supramarginal 952 708 1554 2.713 0.544 0.129 0.027 13 1.0 frontalpole 1395 1063 3219 3.760 0.757 0.113 0.022 39 1.3 temporalpole 1086 555 1314 2.699 0.370 0.073 0.017 6 0.7 transversetemporal 6475 3029 8250 2.707 0.922 0.100 0.041 186 11.2 insula #----------------------------------------- #@# Parcellation Stats 2 rh Wed May 26 00:11:34 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-03 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287397 Total vertex volume 284830 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 1747 728 2107 2.402 0.557 0.104 0.027 27 2.1 G&S_frontomargin 2437 901 2600 2.416 0.469 0.095 0.028 25 2.9 G&S_occipital_inf 3115 1150 3499 2.546 0.465 0.080 0.022 27 2.9 G&S_paracentral 2757 1105 3905 2.847 0.462 0.094 0.022 36 2.5 G&S_subcentral 2611 1086 3374 2.438 0.478 0.114 0.033 52 3.7 G&S_transv_frontopol 5170 2172 6667 2.698 0.495 0.089 0.021 63 4.3 G&S_cingul-Ant 2815 1179 3590 2.829 0.530 0.087 0.023 29 2.7 G&S_cingul-Mid-Ant 2670 1155 3130 2.582 0.442 0.090 0.023 25 2.8 G&S_cingul-Mid-Post 1149 461 2147 3.044 0.621 0.129 0.040 26 2.1 G_cingul-Post-dorsal 649 256 1037 2.807 0.795 0.096 0.030 9 0.8 G_cingul-Post-ventral 4405 1573 4045 2.111 0.502 0.101 0.030 54 5.4 G_cuneus 2275 924 4108 3.097 0.417 0.103 0.029 33 2.7 G_front_inf-Opercular 656 264 1220 3.136 0.468 0.106 0.027 11 0.8 G_front_inf-Orbital 970 391 1586 2.930 0.473 0.101 0.030 14 1.2 G_front_inf-Triangul 8506 3426 13331 2.750 0.457 0.112 0.034 164 13.0 G_front_middle 13419 5508 21877 2.929 0.605 0.105 0.028 208 17.2 G_front_sup 1100 454 1720 3.038 0.874 0.102 0.031 18 1.5 G_Ins_lg&S_cent_ins 1841 772 2713 2.697 1.045 0.136 0.093 48 9.4 G_insular_short 4963 1673 5505 2.413 0.604 0.090 0.028 65 5.9 G_occipital_middle 3479 1243 3154 2.055 0.517 0.090 0.028 40 4.4 G_occipital_sup 4392 1706 7347 3.019 0.628 0.105 0.036 73 6.9 G_oc-temp_lat-fusifor 4801 1839 5001 2.146 0.688 0.105 0.032 67 6.7 G_oc-temp_med-Lingual 1846 741 3540 3.383 0.660 0.074 0.023 12 1.6 G_oc-temp_med-Parahip 4747 1953 8333 2.921 0.508 0.106 0.032 81 6.9 G_orbital 7471 2392 9362 2.843 0.547 0.091 0.033 118 11.1 G_pariet_inf-Angular 5412 1876 6206 2.663 0.449 0.088 0.030 60 7.5 G_pariet_inf-Supramar 4224 1721 5890 2.586 0.520 0.101 0.028 63 5.3 G_parietal_sup 4193 1373 3746 2.139 0.358 0.072 0.023 33 4.2 G_postcentral 5786 1647 6771 2.924 0.488 0.070 0.031 80 7.2 G_precentral 5020 2072 7721 2.763 0.493 0.104 0.028 80 6.2 G_precuneus 1310 517 1927 2.639 0.585 0.110 0.043 47 2.2 G_rectus 711 292 834 2.735 1.290 0.081 0.044 10 1.0 G_subcallosal 883 309 1287 2.947 0.342 0.082 0.021 7 0.8 G_temp_sup-G_T_transv 3247 1233 5314 3.095 0.678 0.093 0.031 41 4.2 G_temp_sup-Lateral 2007 847 3206 3.282 0.947 0.095 0.040 24 4.3 G_temp_sup-Plan_polar 1704 716 2036 2.572 0.523 0.051 0.009 5 0.6 G_temp_sup-Plan_tempo 4883 1871 7256 2.793 0.671 0.100 0.038 76 9.2 G_temporal_inf 5802 2084 8730 2.953 0.660 0.087 0.027 76 6.7 G_temporal_middle 680 268 711 2.714 0.380 0.072 0.016 5 0.5 Lat_Fis-ant-Horizont 245 107 256 2.705 0.362 0.069 0.010 1 0.1 Lat_Fis-ant-Vertical 2512 1059 2238 2.437 0.431 0.080 0.022 22 2.6 Lat_Fis-post 6669 2642 5174 1.768 0.604 0.113 0.037 97 11.4 Pole_occipital 3276 1363 6616 3.322 0.717 0.110 0.035 50 5.3 Pole_temporal 4604 1839 3556 2.173 0.506 0.086 0.028 48 5.2 S_calcarine 5464 2284 4249 2.187 0.440 0.067 0.014 21 3.3 S_central 2072 875 2003 2.403 0.307 0.072 0.014 12 1.2 S_cingul-Marginalis 976 422 893 2.569 0.424 0.068 0.019 3 0.7 S_circular_insula_ant 1866 772 1646 2.600 0.609 0.061 0.013 6 1.1 S_circular_insula_inf 2243 983 2279 2.629 0.494 0.080 0.029 16 2.8 S_circular_insula_sup 1413 590 1342 2.454 0.429 0.059 0.010 5 0.6 S_collat_transv_ant 1202 496 1028 2.313 0.439 0.071 0.011 6 0.6 S_collat_transv_post 3298 1484 3300 2.397 0.377 0.085 0.026 25 4.5 S_front_inf 5632 2459 5567 2.288 0.361 0.074 0.015 34 3.1 S_front_middle 5640 2416 5577 2.506 0.385 0.070 0.015 27 3.2 S_front_sup 917 333 646 2.499 0.656 0.059 0.011 4 0.5 S_interm_prim-Jensen 5460 2303 4857 2.255 0.337 0.078 0.015 38 3.2 S_intrapariet&P_trans 1795 748 1248 2.052 0.370 0.072 0.015 9 1.1 S_oc_middle&Lunatus 3072 1303 2496 2.196 0.297 0.079 0.015 18 1.9 S_oc_sup&transversal 1228 518 1047 2.277 0.375 0.071 0.017 5 0.7 S_occipital_ant 1962 821 1696 2.334 0.282 0.065 0.012 7 0.9 S_oc-temp_lat 3682 1583 3331 2.303 0.514 0.069 0.011 17 1.7 S_oc-temp_med&Lingual 884 374 787 2.358 0.305 0.067 0.013 3 0.4 S_orbital_lateral 905 384 778 2.284 0.474 0.072 0.013 4 0.5 S_orbital_med-olfact 3003 1275 3397 2.523 0.483 0.091 0.021 34 2.5 S_orbital-H_Shaped 4910 2016 4297 2.351 0.327 0.076 0.019 28 4.0 S_parieto_occipital 3562 1411 2020 1.532 0.744 0.089 0.022 45 2.6 S_pericallosal 4529 1906 3818 2.242 0.298 0.074 0.014 27 2.7 S_postcentral 3343 1441 3432 2.636 0.393 0.068 0.012 14 1.9 S_precentral-inf-part 2270 989 2311 2.582 0.495 0.071 0.020 12 2.6 S_precentral-sup-part 648 257 504 2.146 0.315 0.089 0.017 4 0.5 S_suborbital 2345 990 2250 2.459 0.340 0.076 0.017 15 1.6 S_subparietal 2529 1092 2078 2.301 0.421 0.065 0.012 9 1.1 S_temporal_inf 11661 4933 11177 2.478 0.409 0.067 0.013 56 6.4 S_temporal_sup 548 230 400 2.182 0.314 0.081 0.013 3 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 3 rh Wed May 26 00:12:43 UTC 2021 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-03 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287397 Total vertex volume 284830 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 2807 1131 3481 2.462 0.867 0.095 0.022 39 2.4 caudalanteriorcingulate 5613 2355 7180 2.787 0.437 0.086 0.024 51 6.6 caudalmiddlefrontal 5641 2123 5008 2.150 0.471 0.095 0.025 57 6.3 cuneus 1094 468 2148 3.282 0.659 0.083 0.028 8 1.1 entorhinal 7777 3129 10602 2.769 0.607 0.089 0.025 88 8.4 fusiform 16122 6034 17851 2.620 0.513 0.085 0.023 185 15.9 inferiorparietal 9417 3784 12401 2.665 0.637 0.088 0.027 107 11.9 inferiortemporal 3099 1267 3338 2.113 0.992 0.094 0.029 41 3.6 isthmuscingulate 15360 5805 13582 2.094 0.567 0.093 0.027 158 18.9 lateraloccipital 8486 3592 11330 2.606 0.599 0.103 0.032 121 12.5 lateralorbitofrontal 7569 3028 6925 2.037 0.634 0.099 0.029 90 9.3 lingual 4066 1663 5253 2.500 0.746 0.109 0.049 105 9.7 medialorbitofrontal 11704 4596 14682 2.729 0.652 0.076 0.020 102 9.7 middletemporal 1608 654 2015 2.744 0.805 0.060 0.012 7 0.8 parahippocampal 4566 1806 5448 2.623 0.474 0.085 0.022 40 4.6 paracentral 3517 1469 4909 2.815 0.527 0.089 0.022 35 3.2 parsopercularis 1376 580 1969 2.830 0.519 0.085 0.020 13 1.1 parsorbitalis 2930 1222 3859 2.727 0.473 0.090 0.022 30 2.7 parstriangularis 4922 1862 3576 2.034 0.587 0.095 0.034 61 7.2 pericalcarine 12724 4943 12226 2.242 0.451 0.077 0.019 97 10.6 postcentral 3325 1394 4059 2.457 0.781 0.097 0.023 42 3.3 posteriorcingulate 13414 4778 14687 2.752 0.498 0.068 0.021 114 11.6 precentral 11702 4880 14017 2.558 0.449 0.088 0.023 124 11.5 precuneus 2316 955 3054 2.680 0.797 0.092 0.023 31 2.0 rostralanteriorcingulate 13821 5806 16831 2.499 0.447 0.094 0.026 183 15.3 rostralmiddlefrontal 26092 10946 35002 2.697 0.579 0.093 0.024 321 28.0 superiorfrontal 11741 4745 12269 2.335 0.446 0.086 0.021 120 10.0 superiorparietal 13184 5347 18558 2.929 0.748 0.081 0.024 114 14.7 superiortemporal 10281 3802 10685 2.575 0.471 0.081 0.027 101 12.8 supramarginal 1049 367 1286 2.727 0.357 0.081 0.019 8 0.9 transversetemporal 4895 2046 6597 2.870 0.727 0.095 0.037 63 7.8 insula /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label #-------------------------------------------- #@# BA_exvivo Labels rh Wed May 26 00:13:50 UTC 2021 mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 1776 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 5738 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 2734 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 9421 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 898 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4878 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 1702 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 6224 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 3018 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 8765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 1745 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 6218 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 5325 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 17581 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 2994 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 9906 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 2271 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7626 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-03 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 6390 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 11117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-03 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 9556 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 17572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-03 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 2026 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 3958 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-03 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 434 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1472 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-03 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 1102 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 465 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1341 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 952 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3640 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 301 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 807 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2990 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 1014 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 2402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 498 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1987 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 2508 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 9467 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 424 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1436 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 318 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1496 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 4720 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 7952 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 4255 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 7692 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 361 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 629 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 275 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 969 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-03 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white Reading target registration /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 253649 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 419 mri_label2label: Done mris_label2annot --s sub-03 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /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-03/label cmdline mris_label2annot --s sub-03 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-03 hemi rh 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-03/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 180327 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.BA_exvivo.annot mris_label2annot --s sub-03 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /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-03/label cmdline mris_label2annot --s sub-03 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard subject sub-03 hemi rh 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-03/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 212108 unhit vertices Writing annot to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-03 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 287397 Total vertex volume 284830 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 1771 555 1685 2.223 0.401 0.083 0.029 17 2.4 BA1_exvivo 6065 2416 5517 2.260 0.319 0.074 0.016 44 3.9 BA2_exvivo 1796 752 1230 2.071 0.358 0.082 0.018 11 1.4 BA3a_exvivo 3684 1408 3146 2.038 0.420 0.067 0.016 19 2.6 BA3b_exvivo 3614 1172 3801 2.732 0.448 0.064 0.025 32 4.0 BA4a_exvivo 2272 894 2303 2.681 0.357 0.063 0.014 10 1.3 BA4p_exvivo 13869 5342 18971 2.910 0.559 0.085 0.025 153 14.9 BA6_exvivo 6401 2705 8083 2.738 0.495 0.085 0.020 55 6.0 BA44_exvivo 5641 2371 7618 2.716 0.512 0.092 0.028 65 7.3 BA45_exvivo 8263 3069 6026 1.948 0.597 0.098 0.034 106 12.8 V1_exvivo 14477 5676 12454 1.972 0.577 0.104 0.031 177 19.2 V2_exvivo 3902 1473 3425 2.300 0.407 0.078 0.023 29 3.6 MT_exvivo 946 402 1867 3.363 0.569 0.075 0.022 5 0.9 perirhinal_exvivo 621 256 939 3.055 0.565 0.073 0.020 4 0.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-03 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/wm.mgz... reading input surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... reading input pial surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.pial... reading input white surface /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 287397 Total vertex volume 284830 (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) = 1636395 mm^3 (det: 1.190486 ) lhCtxGM: 272546.747 541022.000 diff=-268475.3 pctdiff=-98.506 rhCtxGM: 279131.519 550947.000 diff=-271815.5 pctdiff=-97.379 lhCtxWM: 202331.517 447081.000 diff=-244749.5 pctdiff=-120.965 rhCtxWM: 210022.831 461001.000 diff=-250978.2 pctdiff=-119.500 SubCortGMVol 111835.000 SupraTentVol 1086380.614 (2129326.000) diff=-1042945.386 pctdiff=-96.002 SupraTentVolNotVent 1068967.614 (2111913.000) diff=-1042945.386 pctdiff=-97.566 BrainSegVol 2420274.000 (2416613.000) diff=3661.000 pctdiff=0.151 BrainSegVolNotVent 2397639.000 (1361446.614) diff=1036192.386 pctdiff=43.217 BrainSegVolNotVent 2397639.000 CerebellumVol 285552.000 VentChorVol 17413.000 3rd4th5thCSF 5222.000 CSFVol 1561.000, OptChiasmVol 174.000 MaskVol 2870129.000 1299 388 1143 2.143 0.339 0.077 0.027 11 1.6 BA1_exvivo 3331 1276 3120 2.271 0.303 0.066 0.014 21 1.9 BA2_exvivo 1667 700 1004 2.033 0.304 0.080 0.018 8 1.4 BA3a_exvivo 2771 1111 2118 1.911 0.330 0.065 0.015 13 1.8 BA3b_exvivo 2323 749 2649 2.790 0.540 0.076 0.032 29 3.3 BA4a_exvivo 1802 711 1798 2.714 0.342 0.058 0.013 6 1.0 BA4p_exvivo 8625 3255 11811 2.915 0.563 0.084 0.027 101 10.1 BA6_exvivo 1374 572 2097 2.923 0.520 0.093 0.026 17 1.5 BA44_exvivo 1335 541 2159 2.960 0.495 0.101 0.028 17 1.6 BA45_exvivo 7862 2959 5689 1.940 0.602 0.097 0.034 98 11.9 V1_exvivo 7568 2898 6317 1.902 0.566 0.111 0.035 110 11.6 V2_exvivo 621 212 568 2.245 0.433 0.090 0.033 6 1.0 MT_exvivo 553 231 1076 3.397 0.531 0.064 0.016 2 0.4 perirhinal_exvivo 410 173 620 3.163 0.547 0.074 0.022 2 0.3 entorhinal_exvivo Started at Wed May 26 00:09:14 UTC 2021 Ended at Wed May 26 00:19:14 UTC 2021 #@#%# recon-all-run-time-hours 0.167 recon-all -s sub-03 finished without error at Wed May 26 00:19:14 UTC 2021