Thu Oct 28 22:48:36 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1626.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 767998 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196667928 23658468 164271224 6364696 8738236 165462744 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: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:36-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-02:48:37-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: hritz Machine: node1626.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 Thu Oct 28 22:48:37 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 1 (out of 233808: 0.000428) 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: 1114 vertices, 1217 faces slice 60: 5979 vertices, 6187 faces slice 70: 13605 vertices, 13868 faces slice 80: 22670 vertices, 23047 faces slice 90: 33304 vertices, 33677 faces slice 100: 43819 vertices, 44133 faces slice 110: 54245 vertices, 54610 faces slice 120: 65417 vertices, 65788 faces slice 130: 76535 vertices, 76934 faces slice 140: 86264 vertices, 86648 faces slice 150: 95903 vertices, 96231 faces slice 160: 103527 vertices, 103819 faces slice 170: 110870 vertices, 111161 faces slice 180: 117609 vertices, 117876 faces slice 190: 122790 vertices, 123017 faces slice 200: 126468 vertices, 126609 faces slice 210: 127240 vertices, 127302 faces slice 220: 127240 vertices, 127302 faces slice 230: 127240 vertices, 127302 faces slice 240: 127240 vertices, 127302 faces slice 250: 127240 vertices, 127302 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 127240 voxel in cpt #1: X=-62 [v=127240,e=381906,f=254604] located at (24.710398, -8.915003, 8.406287) For the whole surface: X=-62 [v=127240,e=381906,f=254604] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Oct 28 22:48:40 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 Thu Oct 28 22:48:43 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.2 mm, total surface area = 67384 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 58.963760 mris_inflate stimesec 1.500939 mris_inflate ru_maxrss 206972 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 187252 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 498 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 85763 mris_inflate ru_nivcsw 121 #-------------------------------------------- #@# QSphere rh Thu Oct 28 22:48:56 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 1.03 +- 0.60 (0.00-->9.61) (max @ vno 86005 --> 86006) face area 0.03 +- 0.03 (-0.34-->0.86) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.314... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.061, avgs=0 005/300: dt: 0.9000, rms radial error=176.807, avgs=0 010/300: dt: 0.9000, rms radial error=176.260, avgs=0 015/300: dt: 0.9000, rms radial error=175.542, avgs=0 020/300: dt: 0.9000, rms radial error=174.723, avgs=0 025/300: dt: 0.9000, rms radial error=173.834, avgs=0 030/300: dt: 0.9000, rms radial error=172.913, avgs=0 035/300: dt: 0.9000, rms radial error=171.975, avgs=0 040/300: dt: 0.9000, rms radial error=171.030, avgs=0 045/300: dt: 0.9000, rms radial error=170.083, avgs=0 050/300: dt: 0.9000, rms radial error=169.136, avgs=0 055/300: dt: 0.9000, rms radial error=168.193, avgs=0 060/300: dt: 0.9000, rms radial error=167.253, avgs=0 065/300: dt: 0.9000, rms radial error=166.318, avgs=0 070/300: dt: 0.9000, rms radial error=165.387, avgs=0 075/300: dt: 0.9000, rms radial error=164.461, avgs=0 080/300: dt: 0.9000, rms radial error=163.540, avgs=0 085/300: dt: 0.9000, rms radial error=162.624, avgs=0 090/300: dt: 0.9000, rms radial error=161.712, avgs=0 095/300: dt: 0.9000, rms radial error=160.806, avgs=0 100/300: dt: 0.9000, rms radial error=159.904, avgs=0 105/300: dt: 0.9000, rms radial error=159.007, avgs=0 110/300: dt: 0.9000, rms radial error=158.115, avgs=0 115/300: dt: 0.9000, rms radial error=157.228, avgs=0 120/300: dt: 0.9000, rms radial error=156.345, avgs=0 125/300: dt: 0.9000, rms radial error=155.466, avgs=0 130/300: dt: 0.9000, rms radial error=154.593, avgs=0 135/300: dt: 0.9000, rms radial error=153.724, avgs=0 140/300: dt: 0.9000, rms radial error=152.860, avgs=0 145/300: dt: 0.9000, rms radial error=152.001, avgs=0 150/300: dt: 0.9000, rms radial error=151.146, avgs=0 155/300: dt: 0.9000, rms radial error=150.297, avgs=0 160/300: dt: 0.9000, rms radial error=149.452, avgs=0 165/300: dt: 0.9000, rms radial error=148.611, avgs=0 170/300: dt: 0.9000, rms radial error=147.775, avgs=0 175/300: dt: 0.9000, rms radial error=146.944, avgs=0 180/300: dt: 0.9000, rms radial error=146.117, avgs=0 185/300: dt: 0.9000, rms radial error=145.295, avgs=0 190/300: dt: 0.9000, rms radial error=144.477, avgs=0 195/300: dt: 0.9000, rms radial error=143.664, avgs=0 200/300: dt: 0.9000, rms radial error=142.856, avgs=0 205/300: dt: 0.9000, rms radial error=142.052, avgs=0 210/300: dt: 0.9000, rms radial error=141.252, avgs=0 215/300: dt: 0.9000, rms radial error=140.457, avgs=0 220/300: dt: 0.9000, rms radial error=139.666, avgs=0 225/300: dt: 0.9000, rms radial error=138.880, avgs=0 230/300: dt: 0.9000, rms radial error=138.098, avgs=0 235/300: dt: 0.9000, rms radial error=137.320, avgs=0 240/300: dt: 0.9000, rms radial error=136.546, avgs=0 245/300: dt: 0.9000, rms radial error=135.777, avgs=0 250/300: dt: 0.9000, rms radial error=135.012, avgs=0 255/300: dt: 0.9000, rms radial error=134.252, avgs=0 260/300: dt: 0.9000, rms radial error=133.495, avgs=0 265/300: dt: 0.9000, rms radial error=132.743, avgs=0 270/300: dt: 0.9000, rms radial error=131.995, avgs=0 275/300: dt: 0.9000, rms radial error=131.251, avgs=0 280/300: dt: 0.9000, rms radial error=130.511, avgs=0 285/300: dt: 0.9000, rms radial error=129.775, avgs=0 290/300: dt: 0.9000, rms radial error=129.044, avgs=0 295/300: dt: 0.9000, rms radial error=128.317, avgs=0 300/300: dt: 0.9000, rms radial error=127.593, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14823.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2453.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 251.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00498 epoch 4 (K=640.0), pass 1, starting sse = 16.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00495 final distance error %27.71 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 282.653179 mris_sphere stimesec 1.698094 mris_sphere ru_maxrss 207168 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 505278 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 93608 mris_sphere ru_nivcsw 346 FSRUNTIME@ mris_sphere 0.0197 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy rh Thu Oct 28 22:50:07 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology rh Thu Oct 28 22:50:07 EDT 2021 mris_fix_topology -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-8004 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=-62 (nv=127240, nf=254604, ne=381906, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4148 ambiguous faces found in tessellation segmenting defects... 29 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 29 defects to be corrected 0 vertices coincident reading input surface /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7128 (-4.3564) -vertex loglikelihood: -5.4731 (-2.7365) -normal dot loglikelihood: -3.6065 (-3.6065) -quad curv loglikelihood: -6.4514 (-3.2257) Total Loglikelihood : -24.2438 CORRECTING DEFECT 0 (vertices=67, convex hull=95, v0=20657) After retessellation of defect 0 (v0=20657), euler #=-25 (124720,373102,248357) : difference with theory (-26) = -1 CORRECTING DEFECT 1 (vertices=26, convex hull=54, v0=22672) After retessellation of defect 1 (v0=22672), euler #=-24 (124734,373162,248404) : difference with theory (-25) = -1 CORRECTING DEFECT 2 (vertices=73, convex hull=70, v0=26961) After retessellation of defect 2 (v0=26961), euler #=-23 (124747,373231,248461) : difference with theory (-24) = -1 CORRECTING DEFECT 3 (vertices=39, convex hull=75, v0=27319) After retessellation of defect 3 (v0=27319), euler #=-22 (124776,373349,248551) : difference with theory (-23) = -1 CORRECTING DEFECT 4 (vertices=59, convex hull=107, v0=33914) After retessellation of defect 4 (v0=33914), euler #=-21 (124817,373516,248678) : difference with theory (-22) = -1 CORRECTING DEFECT 5 (vertices=26, convex hull=27, v0=43242) After retessellation of defect 5 (v0=43242), euler #=-20 (124820,373533,248693) : difference with theory (-21) = -1 CORRECTING DEFECT 6 (vertices=493, convex hull=310, v0=47533) normal vector of length zero at vertex 125355 with 3 faces After retessellation of defect 6 (v0=47533), euler #=-20 (124895,373932,249017) : difference with theory (-20) = 0 CORRECTING DEFECT 7 (vertices=29, convex hull=30, v0=53163) After retessellation of defect 7 (v0=53163), euler #=-19 (124897,373946,249030) : difference with theory (-19) = 0 CORRECTING DEFECT 8 (vertices=50, convex hull=83, v0=60077) After retessellation of defect 8 (v0=60077), euler #=-18 (124931,374083,249134) : difference with theory (-18) = 0 CORRECTING DEFECT 9 (vertices=191, convex hull=281, v0=62207) normal vector of length zero at vertex 125639 with 4 faces normal vector of length zero at vertex 125617 with 4 faces normal vector of length zero at vertex 125638 with 3 faces normal vector of length zero at vertex 125624 with 3 faces normal vector of length zero at vertex 125652 with 3 faces After retessellation of defect 9 (v0=62207), euler #=-17 (125064,374613,249532) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=33, convex hull=51, v0=63466) After retessellation of defect 10 (v0=63466), euler #=-16 (125076,374669,249577) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=39, convex hull=49, v0=78485) After retessellation of defect 11 (v0=78485), euler #=-15 (125085,374710,249610) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=15, convex hull=37, v0=80544) After retessellation of defect 12 (v0=80544), euler #=-14 (125086,374727,249627) : difference with theory (-14) = 0 CORRECTING DEFECT 13 (vertices=28, convex hull=71, v0=85119) After retessellation of defect 13 (v0=85119), euler #=-13 (125105,374811,249693) : difference with theory (-13) = 0 CORRECTING DEFECT 14 (vertices=17, convex hull=46, v0=85372) After retessellation of defect 14 (v0=85372), euler #=-12 (125116,374860,249732) : difference with theory (-12) = 0 CORRECTING DEFECT 15 (vertices=108, convex hull=131, v0=85962) After retessellation of defect 15 (v0=85962), euler #=-11 (125167,375066,249888) : difference with theory (-11) = 0 CORRECTING DEFECT 16 (vertices=7, convex hull=18, v0=88160) After retessellation of defect 16 (v0=88160), euler #=-10 (125169,375079,249900) : difference with theory (-10) = 0 CORRECTING DEFECT 17 (vertices=105, convex hull=170, v0=89069) After retessellation of defect 17 (v0=89069), euler #=-9 (125251,375407,250147) : difference with theory (-9) = 0 CORRECTING DEFECT 18 (vertices=167, convex hull=73, v0=89324) After retessellation of defect 18 (v0=89324), euler #=-8 (125276,375513,250229) : difference with theory (-8) = 0 CORRECTING DEFECT 19 (vertices=8, convex hull=16, v0=95573) After retessellation of defect 19 (v0=95573), euler #=-7 (125278,375522,250237) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=31, convex hull=30, v0=96479) After retessellation of defect 20 (v0=96479), euler #=-6 (125287,375558,250265) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=81, convex hull=99, v0=97375) After retessellation of defect 21 (v0=97375), euler #=-5 (125309,375667,250353) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=53, convex hull=88, v0=98981) After retessellation of defect 22 (v0=98981), euler #=-4 (125337,375792,250451) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=24, convex hull=30, v0=104227) After retessellation of defect 23 (v0=104227), euler #=-3 (125342,375817,250472) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=685, convex hull=259, v0=107238) After retessellation of defect 24 (v0=107238), euler #=-2 (125411,376153,250740) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=5, convex hull=19, v0=116369) After retessellation of defect 25 (v0=116369), euler #=-1 (125411,376157,250745) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=25, convex hull=62, v0=122465) After retessellation of defect 26 (v0=122465), euler #=0 (125420,376207,250787) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=20, convex hull=47, v0=123705) After retessellation of defect 27 (v0=123705), euler #=1 (125429,376250,250822) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=44, convex hull=74, v0=126271) After retessellation of defect 28 (v0=126271), euler #=2 (125446,376332,250888) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.07-->15.00) (max @ vno 104739 --> 114905) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.07-->15.00) (max @ vno 104739 --> 114905) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 103 mutations (36.0%), 183 crossovers (64.0%), 278 vertices were eliminated building final representation... 1794 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125446, nf=250888, ne=376332, g=0) writing corrected surface to /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.7 minutes 0 defective edges removing intersecting faces 000: 178 intersecting 001: 4 intersecting mris_fix_topology utimesec 771.439617 mris_fix_topology stimesec 0.404019 mris_fix_topology ru_maxrss 418600 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 430478 mris_fix_topology ru_majflt 4 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 740 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 9150 mris_fix_topology ru_nivcsw 246 FSRUNTIME@ mris_fix_topology rh 0.2121 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 125446 - 376332 + 250888 = 2 --> 0 holes F =2V-4: 250888 = 250892-4 (0) 2E=3F: 752664 = 752664 (0) total defect index = 0 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 17 intersecting 001: 14 intersecting 002: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Oct 28 23:02:55 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-8004 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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/mri/filled.mgz... reading volume /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/mri/brain.finalsurfs.mgz... reading volume /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/mri/../mri/aseg.presurf.mgz... reading volume /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/mri/wm.mgz... 19054 bright wm thresholded. 4 bright non-wm voxels segmented. reading original surface position from /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/rh.orig... computing class statistics... border white: 234030 voxels (1.39%) border gray 258607 voxels (1.54%) WM (103.0): 103.3 +- 5.6 [70.0 --> 110.0] GM (86.0) : 85.4 +- 8.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 75.6 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 67.2 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 75.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 58.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->7.07) (max @ vno 104739 --> 114905) face area 0.28 +- 0.12 (0.00-->4.41) mean absolute distance = 0.77 +- 0.96 3831 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-3.5, GM=84+-5.2 mean inside = 100.5, mean outside = 88.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.9, 26 (26) missing vertices, mean dist 0.3 [0.7 (%34.6)->0.8 (%65.4))] %60 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.11-->6.74) (max @ vno 104739 --> 114905) face area 0.28 +- 0.13 (0.00-->5.17) mean absolute distance = 0.37 +- 0.60 2614 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1758853.0, rms=7.156 001: dt: 0.5000, sse=1127421.5, rms=5.082 (28.987%) 002: dt: 0.5000, sse=836165.4, rms=3.727 (26.653%) 003: dt: 0.5000, sse=697206.6, rms=2.860 (23.280%) 004: dt: 0.5000, sse=630401.2, rms=2.320 (18.868%) 005: dt: 0.5000, sse=604584.1, rms=2.032 (12.427%) 006: dt: 0.5000, sse=588402.6, rms=1.886 (7.153%) 007: dt: 0.5000, sse=584972.1, rms=1.828 (3.097%) rms = 1.79, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=581099.6, rms=1.790 (2.096%) 009: dt: 0.2500, sse=553204.4, rms=1.261 (29.526%) 010: dt: 0.2500, sse=546368.2, rms=1.194 (5.322%) rms = 1.18, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=547548.8, rms=1.181 (1.109%) rms = 1.17, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=545164.5, rms=1.170 (0.903%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=93.0, 19 (1) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.2 (%28.0))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.13-->6.62) (max @ vno 104739 --> 114905) face area 0.35 +- 0.16 (0.00-->7.09) mean absolute distance = 0.28 +- 0.39 3241 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=895078.2, rms=3.233 013: dt: 0.5000, sse=730709.1, rms=1.936 (40.117%) 014: dt: 0.5000, sse=692632.2, rms=1.502 (22.431%) 015: dt: 0.5000, sse=681557.1, rms=1.355 (9.754%) rms = 1.34, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=679130.3, rms=1.345 (0.783%) 017: dt: 0.2500, sse=666423.9, rms=1.046 (22.176%) rms = 1.02, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=665624.8, rms=1.018 (2.686%) rms = 1.01, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=664763.9, rms=1.013 (0.562%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=94.8, 24 (1) missing vertices, mean dist -0.2 [0.3 (%73.8)->0.2 (%26.2))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.04-->6.52) (max @ vno 104739 --> 114905) face area 0.34 +- 0.16 (0.00-->7.12) mean absolute distance = 0.21 +- 0.31 3482 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=760855.9, rms=2.449 020: dt: 0.5000, sse=661774.3, rms=1.347 (44.993%) 021: dt: 0.5000, sse=651583.6, rms=1.208 (10.316%) rms = 1.21, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=651183.9, rms=1.208 (0.008%) 023: dt: 0.2500, sse=639711.4, rms=0.955 (20.905%) rms = 0.94, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=639417.1, rms=0.941 (1.500%) rms = 0.94, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=640257.8, rms=0.937 (0.391%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=95.4, 33 (1) missing vertices, mean dist -0.1 [0.2 (%58.2)->0.2 (%41.8))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=640526.2, rms=1.189 026: dt: 0.5000, sse=620411.2, rms=0.801 (32.608%) rms = 1.02, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=617733.2, rms=0.739 (7.751%) rms = 0.75, time step reduction 2 of 3 to 0.125... rms = 0.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=617313.2, rms=0.736 (0.388%) positioning took 0.3 minutes generating cortex label... 5 non-cortical segments detected only using segment with 6470 vertices erasing segment 1 (vno[0] = 88732) erasing segment 2 (vno[0] = 90689) erasing segment 3 (vno[0] = 91640) erasing segment 4 (vno[0] = 109445) writing cortex label to /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/label/rh.cortex.label... writing curvature file /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/rh.curv writing smoothed area to rh.area writing curvature file /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->6.48) (max @ vno 104739 --> 114905) face area 0.33 +- 0.16 (0.00-->7.04) refinement took 2.8 minutes #-------------------------------------------- #@# Smooth2 rh Thu Oct 28 23:05:42 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 Thu Oct 28 23:05:45 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_inflate -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.2 mm, total surface area = 76251 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.2 minutes mris_inflate utimesec 58.207402 mris_inflate stimesec 1.133266 mris_inflate ru_maxrss 204260 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 216653 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 83384 mris_inflate ru_nivcsw 116 #-------------------------------------------- #@# Curv .H and .K rh Thu Oct 28 23:05:59 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf mris_curvature -w rh.white.preaparc total integrated curvature = 7.896*4pi (99.230) --> -7 handles ICI = 141.9, FI = 1589.5, variation=24552.718 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 149 vertices thresholded to be in k1 ~ [-0.32 0.41], k2 ~ [-0.12 0.09] total integrated curvature = 0.521*4pi (6.545) --> 0 handles ICI = 1.4, FI = 8.9, variation=149.730 104 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 137 vertices thresholded to be in [-0.16 0.21] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats rh Thu Oct 28 23:06:45 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-8004 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-8004/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 [ 223 ] Gb_filter = 0 WARN: S lookup min: -0.078405 WARN: S explicit min: 0.000000 vertex = 314 #-------------------------------------------- #@# Sphere rh Thu Oct 28 23:06:48 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_sphere -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 0.293... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node1, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.00 pass 1: epoch 2 of 3 starting distance error %19.98 unfolding complete - removing small folds... starting distance error %19.94 removing remaining folds... final distance error %19.95 MRISunfold() return, current seed 1234 -01: dt=0.0000, 127 negative triangles 159: dt=0.9900, 127 negative triangles 160: dt=0.9900, 53 negative triangles 161: dt=0.9900, 37 negative triangles 162: dt=0.9900, 33 negative triangles 163: dt=0.9900, 33 negative triangles 164: dt=0.9900, 37 negative triangles 165: dt=0.9900, 27 negative triangles 166: dt=0.9900, 25 negative triangles 167: dt=0.9900, 28 negative triangles 168: dt=0.9900, 28 negative triangles 169: dt=0.9900, 23 negative triangles 170: dt=0.9900, 27 negative triangles 171: dt=0.9900, 17 negative triangles 172: dt=0.9900, 20 negative triangles 173: dt=0.9900, 19 negative triangles 174: dt=0.9900, 15 negative triangles 175: dt=0.9900, 17 negative triangles 176: dt=0.9900, 11 negative triangles 177: dt=0.9900, 6 negative triangles 178: dt=0.9900, 6 negative triangles 179: dt=0.9900, 3 negative triangles 180: dt=0.9900, 4 negative triangles 181: dt=0.9900, 4 negative triangles 182: dt=0.9900, 3 negative triangles 183: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.10 hours mris_sphere utimesec 2330.088971 mris_sphere stimesec 5.385205 mris_sphere ru_maxrss 283196 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 2346002 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 135095 mris_sphere ru_nivcsw 2257 FSRUNTIME@ mris_sphere 0.1019 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Oct 28 23:12:54 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1626.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Thu Oct 28 23:12:55 EDT 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri Oct 29 09:02:56 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1109.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 768127 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196684172 18523748 169180924 7207576 8979500 169810896 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: 2021/10/29-13:02:56-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-13:02:56-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-13:02:56-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:56-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/10/29-13:02:57-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: hritz Machine: node1109.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 ####################################### #-------------------------------------------- #@# Surf Reg rh Fri Oct 29 09:02:57 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1109.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Fri Oct 29 09:02:57 EDT 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Nov 11 21:58:51 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1325.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 768070 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196669632 28687392 158872540 7010468 9109700 159834832 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: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:51-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-02:58:52-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: hritz Machine: node1325.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 ####################################### #-------------------------------------------- #@# Surf Reg rh Thu Nov 11 21:58:52 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1325.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Thu Nov 11 21:58:52 EST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri Nov 12 10:08:55 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1628.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 767998 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196667928 40486612 147372944 6625892 8808372 148368336 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: 2021/11/12-15:08:55-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-15:08:56-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: hritz Machine: node1628.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 ####################################### #-------------------------------------------- #@# Surf Reg rh Fri Nov 12 10:08:56 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1628.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Fri Nov 12 10:08:56 EST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri Nov 12 12:34:43 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1648.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 767933 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196667928 41342256 146599652 6752712 8726020 147378068 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: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-17:34:43-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: hritz Machine: node1648.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 ####################################### #-------------------------------------------- #@# Surf Reg rh Fri Nov 12 12:34:43 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1648.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Fri Nov 12 12:34:44 EST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri Nov 12 18:14:23 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1123.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 768032 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 196677396 23182684 164442656 6880976 9052056 165463300 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: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/12-23:14:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: hritz Machine: node1123.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 ####################################### #-------------------------------------------- #@# Surf Reg rh Fri Nov 12 18:14:23 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1123.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Fri Nov 12 18:14:23 EST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri Nov 12 22:03:58 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-8004 -sd /data/bids/derivatives/fmriprep-20.2.6/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere subjid sub-8004 setenv SUBJECTS_DIR /data/bids/derivatives/fmriprep-20.2.6/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 node1344.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 500000 kbytes coredumpsize 0 kbytes memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4096 maxlocks unlimited maxsignal 1541994 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 394849020 21718872 364422448 6818844 8707700 364739680 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: 2021/11/13-03:03:58-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/13-03:03:58-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/11/13-03:03:59-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: hritz Machine: node1344.oscar.ccv.brown.edu Platform: Linux PlatformVersion: 3.10.0-1062.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 ####################################### #-------------------------------------------- #@# Surf Reg rh Fri Nov 12 22:03:59 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cmdline mris_register -curv -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/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... mrisFindNeighbors: ../surf/rh.sphere: face[224074].v[0] = 112919, but face 224074 not in vertex 112919 face list Linux node1344.oscar.ccv.brown.edu 3.10.0-1062.el7.x86_64 #1 SMP Thu Jul 18 20:25:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-8004 exited with ERRORS at Fri Nov 12 22:03:59 EST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting