Thu Oct 28 22:48:37 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -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 23668864 164260912 6364696 8738152 165452432 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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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: 2021/10/29-02:48:37-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 lh Thu Oct 28 22:48:37 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 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 = 3 (out of 233040: 0.001287) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 501 vertices, 564 faces slice 60: 4729 vertices, 4894 faces slice 70: 11020 vertices, 11278 faces slice 80: 19232 vertices, 19541 faces slice 90: 28111 vertices, 28479 faces slice 100: 38230 vertices, 38552 faces slice 110: 48709 vertices, 49102 faces slice 120: 59924 vertices, 60328 faces slice 130: 71081 vertices, 71480 faces slice 140: 82047 vertices, 82483 faces slice 150: 92108 vertices, 92474 faces slice 160: 101017 vertices, 101344 faces slice 170: 108217 vertices, 108512 faces slice 180: 115216 vertices, 115469 faces slice 190: 121311 vertices, 121567 faces slice 200: 125693 vertices, 125876 faces slice 210: 127032 vertices, 127090 faces slice 220: 127032 vertices, 127090 faces slice 230: 127032 vertices, 127090 faces slice 240: 127032 vertices, 127090 faces slice 250: 127032 vertices, 127090 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 127032 voxel in cpt #1: X=-58 [v=127032,e=381270,f=254180] located at (-28.228714, -4.894885, 7.205224) For the whole surface: X=-58 [v=127032,e=381270,f=254180] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh 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/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Oct 28 22:48:44 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.7 mm, total surface area = 66600 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 57.323509 mris_inflate stimesec 1.591596 mris_inflate ru_maxrss 207040 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 155068 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 94587 mris_inflate ru_nivcsw 51 #-------------------------------------------- #@# QSphere lh 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/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.58 (0.00-->6.81) (max @ vno 38859 --> 39832) face area 0.03 +- 0.03 (-0.14-->0.69) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.312... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.409, avgs=0 005/300: dt: 0.9000, rms radial error=177.150, avgs=0 010/300: dt: 0.9000, rms radial error=176.593, avgs=0 015/300: dt: 0.9000, rms radial error=175.862, avgs=0 020/300: dt: 0.9000, rms radial error=175.029, avgs=0 025/300: dt: 0.9000, rms radial error=174.139, avgs=0 030/300: dt: 0.9000, rms radial error=173.216, avgs=0 035/300: dt: 0.9000, rms radial error=172.277, avgs=0 040/300: dt: 0.9000, rms radial error=171.330, avgs=0 045/300: dt: 0.9000, rms radial error=170.379, avgs=0 050/300: dt: 0.9000, rms radial error=169.429, avgs=0 055/300: dt: 0.9000, rms radial error=168.482, avgs=0 060/300: dt: 0.9000, rms radial error=167.539, avgs=0 065/300: dt: 0.9000, rms radial error=166.599, avgs=0 070/300: dt: 0.9000, rms radial error=165.664, avgs=0 075/300: dt: 0.9000, rms radial error=164.734, avgs=0 080/300: dt: 0.9000, rms radial error=163.809, avgs=0 085/300: dt: 0.9000, rms radial error=162.889, avgs=0 090/300: dt: 0.9000, rms radial error=161.974, avgs=0 095/300: dt: 0.9000, rms radial error=161.064, avgs=0 100/300: dt: 0.9000, rms radial error=160.159, avgs=0 105/300: dt: 0.9000, rms radial error=159.258, avgs=0 110/300: dt: 0.9000, rms radial error=158.362, avgs=0 115/300: dt: 0.9000, rms radial error=157.472, avgs=0 120/300: dt: 0.9000, rms radial error=156.586, avgs=0 125/300: dt: 0.9000, rms radial error=155.705, avgs=0 130/300: dt: 0.9000, rms radial error=154.829, avgs=0 135/300: dt: 0.9000, rms radial error=153.958, avgs=0 140/300: dt: 0.9000, rms radial error=153.094, avgs=0 145/300: dt: 0.9000, rms radial error=152.234, avgs=0 150/300: dt: 0.9000, rms radial error=151.379, avgs=0 155/300: dt: 0.9000, rms radial error=150.528, avgs=0 160/300: dt: 0.9000, rms radial error=149.682, avgs=0 165/300: dt: 0.9000, rms radial error=148.841, avgs=0 170/300: dt: 0.9000, rms radial error=148.004, avgs=0 175/300: dt: 0.9000, rms radial error=147.172, avgs=0 180/300: dt: 0.9000, rms radial error=146.344, avgs=0 185/300: dt: 0.9000, rms radial error=145.521, avgs=0 190/300: dt: 0.9000, rms radial error=144.702, avgs=0 195/300: dt: 0.9000, rms radial error=143.888, avgs=0 200/300: dt: 0.9000, rms radial error=143.078, avgs=0 205/300: dt: 0.9000, rms radial error=142.273, avgs=0 210/300: dt: 0.9000, rms radial error=141.472, avgs=0 215/300: dt: 0.9000, rms radial error=140.676, avgs=0 220/300: dt: 0.9000, rms radial error=139.884, avgs=0 225/300: dt: 0.9000, rms radial error=139.097, avgs=0 230/300: dt: 0.9000, rms radial error=138.314, avgs=0 235/300: dt: 0.9000, rms radial error=137.535, avgs=0 240/300: dt: 0.9000, rms radial error=136.760, avgs=0 245/300: dt: 0.9000, rms radial error=135.990, avgs=0 250/300: dt: 0.9000, rms radial error=135.224, avgs=0 255/300: dt: 0.9000, rms radial error=134.463, avgs=0 260/300: dt: 0.9000, rms radial error=133.706, avgs=0 265/300: dt: 0.9000, rms radial error=132.952, avgs=0 270/300: dt: 0.9000, rms radial error=132.203, avgs=0 275/300: dt: 0.9000, rms radial error=131.459, avgs=0 280/300: dt: 0.9000, rms radial error=130.718, avgs=0 285/300: dt: 0.9000, rms radial error=129.982, avgs=0 290/300: dt: 0.9000, rms radial error=129.250, avgs=0 295/300: dt: 0.9000, rms radial error=128.521, avgs=0 300/300: dt: 0.9000, rms radial error=127.797, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14839.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2461.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 248.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00836 epoch 4 (K=640.0), pass 1, starting sse = 13.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/17 = 0.00915 final distance error %26.49 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 283.282335 mris_sphere stimesec 1.480472 mris_sphere ru_maxrss 207292 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 415533 mris_sphere ru_majflt 3 mris_sphere ru_nswap 0 mris_sphere ru_inblock 510 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 82804 mris_sphere ru_nivcsw 180 FSRUNTIME@ mris_sphere 0.0199 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Thu Oct 28 22:50:08 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Thu Oct 28 22:50:08 EDT 2021 mris_fix_topology -rusage /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-8004 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-58 (nv=127032, nf=254180, ne=381270, g=30) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 3216 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 44 defects to be corrected 0 vertices coincident reading input surface /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7137 (-4.3569) -vertex loglikelihood: -5.4360 (-2.7180) -normal dot loglikelihood: -3.6523 (-3.6523) -quad curv loglikelihood: -6.2468 (-3.1234) Total Loglikelihood : -24.0488 CORRECTING DEFECT 0 (vertices=35, convex hull=81, v0=6369) After retessellation of defect 0 (v0=6369), euler #=-41 (124957,373740,248742) : difference with theory (-41) = 0 CORRECTING DEFECT 1 (vertices=30, convex hull=62, v0=8862) After retessellation of defect 1 (v0=8862), euler #=-40 (124967,373798,248791) : difference with theory (-40) = 0 CORRECTING DEFECT 2 (vertices=37, convex hull=63, v0=13375) After retessellation of defect 2 (v0=13375), euler #=-39 (124992,373898,248867) : difference with theory (-39) = 0 CORRECTING DEFECT 3 (vertices=62, convex hull=90, v0=18279) After retessellation of defect 3 (v0=18279), euler #=-38 (125027,374040,248975) : difference with theory (-38) = 0 CORRECTING DEFECT 4 (vertices=63, convex hull=98, v0=24665) After retessellation of defect 4 (v0=24665), euler #=-37 (125073,374222,249112) : difference with theory (-37) = 0 CORRECTING DEFECT 5 (vertices=23, convex hull=59, v0=25405) After retessellation of defect 5 (v0=25405), euler #=-36 (125088,374289,249165) : difference with theory (-36) = 0 CORRECTING DEFECT 6 (vertices=6, convex hull=21, v0=27679) After retessellation of defect 6 (v0=27679), euler #=-35 (125090,374300,249175) : difference with theory (-35) = 0 CORRECTING DEFECT 7 (vertices=16, convex hull=51, v0=27715) After retessellation of defect 7 (v0=27715), euler #=-34 (125100,374349,249215) : difference with theory (-34) = 0 CORRECTING DEFECT 8 (vertices=40, convex hull=77, v0=28254) After retessellation of defect 8 (v0=28254), euler #=-33 (125127,374462,249302) : difference with theory (-33) = 0 CORRECTING DEFECT 9 (vertices=32, convex hull=63, v0=32418) After retessellation of defect 9 (v0=32418), euler #=-32 (125146,374544,249366) : difference with theory (-32) = 0 CORRECTING DEFECT 10 (vertices=36, convex hull=58, v0=42083) After retessellation of defect 10 (v0=42083), euler #=-31 (125173,374651,249447) : difference with theory (-31) = 0 CORRECTING DEFECT 11 (vertices=186, convex hull=162, v0=45992) normal vector of length zero at vertex 125425 with 3 faces normal vector of length zero at vertex 125375 with 3 faces normal vector of length zero at vertex 125375 with 3 faces normal vector of length zero at vertex 125372 with 3 faces normal vector of length zero at vertex 125424 with 3 faces normal vector of length zero at vertex 125424 with 3 faces normal vector of length zero at vertex 125424 with 3 faces normal vector of length zero at vertex 125424 with 3 faces normal vector of length zero at vertex 125424 with 3 faces After retessellation of defect 11 (v0=45992), euler #=-30 (125191,374779,249558) : difference with theory (-30) = 0 CORRECTING DEFECT 12 (vertices=14, convex hull=17, v0=46100) After retessellation of defect 12 (v0=46100), euler #=-29 (125192,374786,249565) : difference with theory (-29) = 0 CORRECTING DEFECT 13 (vertices=84, convex hull=66, v0=47210) After retessellation of defect 13 (v0=47210), euler #=-28 (125201,374836,249607) : difference with theory (-28) = 0 CORRECTING DEFECT 14 (vertices=13, convex hull=29, v0=49767) After retessellation of defect 14 (v0=49767), euler #=-27 (125203,374851,249621) : difference with theory (-27) = 0 CORRECTING DEFECT 15 (vertices=19, convex hull=29, v0=50668) After retessellation of defect 15 (v0=50668), euler #=-26 (125206,374868,249636) : difference with theory (-26) = 0 CORRECTING DEFECT 16 (vertices=31, convex hull=63, v0=51176) After retessellation of defect 16 (v0=51176), euler #=-25 (125219,374931,249687) : difference with theory (-25) = 0 CORRECTING DEFECT 17 (vertices=13, convex hull=25, v0=55289) After retessellation of defect 17 (v0=55289), euler #=-24 (125222,374948,249702) : difference with theory (-24) = 0 CORRECTING DEFECT 18 (vertices=21, convex hull=48, v0=60802) After retessellation of defect 18 (v0=60802), euler #=-23 (125235,375004,249746) : difference with theory (-23) = 0 CORRECTING DEFECT 19 (vertices=107, convex hull=104, v0=65484) After retessellation of defect 19 (v0=65484), euler #=-22 (125284,375197,249891) : difference with theory (-22) = 0 CORRECTING DEFECT 20 (vertices=33, convex hull=70, v0=75477) After retessellation of defect 20 (v0=75477), euler #=-21 (125297,375262,249944) : difference with theory (-21) = 0 CORRECTING DEFECT 21 (vertices=42, convex hull=37, v0=80529) After retessellation of defect 21 (v0=80529), euler #=-20 (125304,375297,249973) : difference with theory (-20) = 0 CORRECTING DEFECT 22 (vertices=49, convex hull=58, v0=80636) After retessellation of defect 22 (v0=80636), euler #=-19 (125313,375347,250015) : difference with theory (-19) = 0 CORRECTING DEFECT 23 (vertices=13, convex hull=22, v0=82084) After retessellation of defect 23 (v0=82084), euler #=-18 (125314,375359,250027) : difference with theory (-18) = 0 CORRECTING DEFECT 24 (vertices=81, convex hull=97, v0=83084) After retessellation of defect 24 (v0=83084), euler #=-17 (125362,375542,250163) : difference with theory (-17) = 0 CORRECTING DEFECT 25 (vertices=68, convex hull=63, v0=84033) After retessellation of defect 25 (v0=84033), euler #=-16 (125391,375657,250250) : difference with theory (-16) = 0 CORRECTING DEFECT 26 (vertices=16, convex hull=31, v0=87034) After retessellation of defect 26 (v0=87034), euler #=-15 (125395,375685,250275) : difference with theory (-15) = 0 CORRECTING DEFECT 27 (vertices=13, convex hull=27, v0=88779) After retessellation of defect 27 (v0=88779), euler #=-14 (125397,375700,250289) : difference with theory (-14) = 0 CORRECTING DEFECT 28 (vertices=63, convex hull=120, v0=89177) After retessellation of defect 28 (v0=89177), euler #=-13 (125430,375856,250413) : difference with theory (-13) = 0 CORRECTING DEFECT 29 (vertices=202, convex hull=29, v0=93904) After retessellation of defect 29 (v0=93904), euler #=-12 (125437,375888,250439) : difference with theory (-12) = 0 CORRECTING DEFECT 30 (vertices=57, convex hull=25, v0=94138) After retessellation of defect 30 (v0=94138), euler #=-11 (125441,375909,250457) : difference with theory (-11) = 0 CORRECTING DEFECT 31 (vertices=70, convex hull=109, v0=97594) After retessellation of defect 31 (v0=97594), euler #=-10 (125477,376065,250578) : difference with theory (-10) = 0 CORRECTING DEFECT 32 (vertices=35, convex hull=66, v0=103339) After retessellation of defect 32 (v0=103339), euler #=-9 (125491,376135,250635) : difference with theory (-9) = 0 CORRECTING DEFECT 33 (vertices=60, convex hull=110, v0=104791) After retessellation of defect 33 (v0=104791), euler #=-8 (125514,376251,250729) : difference with theory (-8) = 0 CORRECTING DEFECT 34 (vertices=69, convex hull=100, v0=111114) After retessellation of defect 34 (v0=111114), euler #=-7 (125539,376367,250821) : difference with theory (-7) = 0 CORRECTING DEFECT 35 (vertices=67, convex hull=101, v0=116390) After retessellation of defect 35 (v0=116390), euler #=-6 (125567,376498,250925) : difference with theory (-6) = 0 CORRECTING DEFECT 36 (vertices=32, convex hull=30, v0=116988) After retessellation of defect 36 (v0=116988), euler #=-5 (125573,376528,250950) : difference with theory (-5) = 0 CORRECTING DEFECT 37 (vertices=53, convex hull=62, v0=119346) After retessellation of defect 37 (v0=119346), euler #=-4 (125587,376590,250999) : difference with theory (-4) = 0 CORRECTING DEFECT 38 (vertices=60, convex hull=98, v0=119802) After retessellation of defect 38 (v0=119802), euler #=-3 (125620,376729,251106) : difference with theory (-3) = 0 CORRECTING DEFECT 39 (vertices=45, convex hull=70, v0=121750) After retessellation of defect 39 (v0=121750), euler #=-2 (125644,376832,251186) : difference with theory (-2) = 0 CORRECTING DEFECT 40 (vertices=38, convex hull=107, v0=123624) After retessellation of defect 40 (v0=123624), euler #=-1 (125663,376933,251269) : difference with theory (-1) = 0 CORRECTING DEFECT 41 (vertices=24, convex hull=51, v0=125736) After retessellation of defect 41 (v0=125736), euler #=0 (125672,376979,251307) : difference with theory (0) = 0 CORRECTING DEFECT 42 (vertices=16, convex hull=27, v0=126139) After retessellation of defect 42 (v0=126139), euler #=1 (125674,376995,251322) : difference with theory (1) = 0 CORRECTING DEFECT 43 (vertices=23, convex hull=59, v0=126850) After retessellation of defect 43 (v0=126850), euler #=2 (125686,377052,251368) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.08-->8.20) (max @ vno 47823 --> 48987) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.08-->8.20) (max @ vno 47823 --> 48987) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 147 mutations (34.5%), 279 crossovers (65.5%), 140 vertices were eliminated building final representation... 1346 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125686, nf=251368, ne=377052, g=0) writing corrected surface to /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.8 minutes 0 defective edges removing intersecting faces 000: 263 intersecting 001: 7 intersecting mris_fix_topology utimesec 777.568508 mris_fix_topology stimesec 0.369983 mris_fix_topology ru_maxrss 417488 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 375284 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 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 3760 mris_fix_topology ru_nivcsw 2498 FSRUNTIME@ mris_fix_topology lh 0.2139 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 125686 - 377052 + 251368 = 2 --> 0 holes F =2V-4: 251368 = 251372-4 (0) 2E=3F: 754104 = 754104 (0) total defect index = 0 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Oct 28 23:03:01 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 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /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/lh.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 74.6 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 66.2 (was 40) setting MAX_GRAY to 100.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 74.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 57.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.57) (max @ vno 48987 --> 125186) face area 0.28 +- 0.12 (0.00-->4.70) mean absolute distance = 0.78 +- 0.94 3800 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-3.5, GM=83+-6.1 mean inside = 100.5, mean outside = 88.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.4, 31 (31) missing vertices, mean dist 0.4 [0.6 (%32.6)->0.9 (%67.4))] %65 local maxima, %31 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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.09-->3.56) (max @ vno 46784 --> 50284) face area 0.28 +- 0.13 (0.00-->3.70) mean absolute distance = 0.37 +- 0.58 3506 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1831959.0, rms=7.370 001: dt: 0.5000, sse=1182740.0, rms=5.317 (27.853%) 002: dt: 0.5000, sse=869636.4, rms=3.928 (26.134%) 003: dt: 0.5000, sse=712802.9, rms=2.997 (23.701%) 004: dt: 0.5000, sse=637098.1, rms=2.407 (19.665%) 005: dt: 0.5000, sse=602276.3, rms=2.081 (13.556%) 006: dt: 0.5000, sse=587587.9, rms=1.920 (7.761%) 007: dt: 0.5000, sse=581896.9, rms=1.844 (3.949%) rms = 1.81, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=581084.6, rms=1.810 (1.849%) 009: dt: 0.2500, sse=547791.9, rms=1.287 (28.908%) 010: dt: 0.2500, sse=556227.9, rms=1.223 (4.967%) rms = 1.21, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=543738.5, rms=1.208 (1.159%) rms = 1.20, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=543425.6, rms=1.198 (0.874%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.7, 27 (4) missing vertices, mean dist -0.2 [0.4 (%73.3)->0.3 (%26.7))] %78 local maxima, %18 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 (0.09-->3.68) (max @ vno 27466 --> 27467) face area 0.35 +- 0.16 (0.00-->4.89) mean absolute distance = 0.27 +- 0.37 3252 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=921989.2, rms=3.401 013: dt: 0.5000, sse=747313.9, rms=2.086 (38.648%) 014: dt: 0.5000, sse=707886.4, rms=1.629 (21.927%) 015: dt: 0.5000, sse=688922.9, rms=1.449 (11.062%) rms = 1.40, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=684658.8, rms=1.403 (3.184%) 017: dt: 0.2500, sse=668651.8, rms=1.092 (22.163%) rms = 1.05, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=667886.2, rms=1.048 (3.998%) rms = 1.04, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=666418.8, rms=1.038 (1.011%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=94.5, 15 (2) missing vertices, mean dist -0.2 [0.3 (%74.4)->0.2 (%25.6))] %87 local maxima, % 8 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 (0.11-->3.91) (max @ vno 27466 --> 27467) face area 0.34 +- 0.16 (0.00-->4.80) mean absolute distance = 0.21 +- 0.30 3303 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=765649.9, rms=2.494 020: dt: 0.5000, sse=661673.1, rms=1.360 (45.454%) 021: dt: 0.5000, sse=651522.8, rms=1.218 (10.467%) rms = 1.21, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=649666.6, rms=1.209 (0.710%) 023: dt: 0.2500, sse=638320.4, rms=0.961 (20.492%) rms = 0.95, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=637924.4, rms=0.950 (1.196%) rms = 0.95, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=637929.2, rms=0.947 (0.285%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=95.1, 18 (1) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))] %90 local maxima, % 5 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/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=636634.9, rms=1.160 026: dt: 0.5000, sse=619148.8, rms=0.801 (30.930%) rms = 1.02, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=617024.3, rms=0.745 (7.060%) rms = 0.76, 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=616887.8, rms=0.742 (0.332%) positioning took 0.3 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6854 vertices erasing segment 0 (vno[0] = 26474) erasing segment 2 (vno[0] = 71735) erasing segment 3 (vno[0] = 90603) erasing segment 4 (vno[0] = 90610) erasing segment 5 (vno[0] = 91483) erasing segment 6 (vno[0] = 95253) writing cortex label to /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/label/lh.cortex.label... writing curvature file /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/lh.curv writing smoothed area to lh.area writing curvature file /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf/lh.area vertex spacing 0.89 +- 0.25 (0.03-->3.97) (max @ vno 27466 --> 27467) face area 0.33 +- 0.16 (0.00-->4.73) refinement took 2.8 minutes #-------------------------------------------- #@# Smooth2 lh Thu Oct 28 23:05:50 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Oct 28 23:05:53 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.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.8 mm, total surface area = 76239 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.2 minutes mris_inflate utimesec 53.476254 mris_inflate stimesec 1.448607 mris_inflate ru_maxrss 205036 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 172517 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 90403 mris_inflate ru_nivcsw 141 #-------------------------------------------- #@# Curv .H and .K lh Thu Oct 28 23:06:05 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf mris_curvature -w lh.white.preaparc total integrated curvature = 0.144*4pi (1.807) --> 1 handles ICI = 136.0, FI = 1580.2, variation=24368.305 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 154 vertices thresholded to be in k1 ~ [-0.20 0.65], k2 ~ [-0.12 0.05] total integrated curvature = 0.582*4pi (7.308) --> 0 handles ICI = 1.4, FI = 8.4, variation=144.753 97 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 120 vertices thresholded to be in [-0.13 0.20] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Thu Oct 28 23:06:52 EDT 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-8004 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-8004/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 216 ] Gb_filter = 0 WARN: S lookup min: -0.206529 WARN: S explicit min: 0.000000 vertex = 195 #-------------------------------------------- #@# Sphere lh Thu Oct 28 23:06:54 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.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.291... 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 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %40.94 pass 1: epoch 2 of 3 starting distance error %19.59 unfolding complete - removing small folds... starting distance error %19.48 removing remaining folds... final distance error %19.51 MRISunfold() return, current seed 1234 -01: dt=0.0000, 81 negative triangles 120: dt=0.9900, 81 negative triangles 121: dt=0.9900, 22 negative triangles 122: dt=0.9900, 17 negative triangles 123: dt=0.9900, 16 negative triangles 124: dt=0.9900, 12 negative triangles 125: dt=0.9900, 8 negative triangles 126: dt=0.9900, 6 negative triangles 127: dt=0.9900, 6 negative triangles 128: dt=0.9900, 3 negative triangles 129: dt=0.9900, 4 negative triangles 130: dt=0.9900, 4 negative triangles 131: dt=0.9900, 4 negative triangles 132: dt=0.9900, 4 negative triangles 133: dt=0.9900, 4 negative triangles 134: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.06 hours recon-all -s sub-8004 exited with ERRORS at Thu Oct 28 23:10:37 EDT 2021 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 lh -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 18519232 169185440 7207576 8979500 169815412 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: 2021/10/29-13:02:56-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: 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: 2021/10/29-13:02:56-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: 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: 2021/10/29-13:02:56-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: 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: 2021/10/29-13:02:56-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: 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: 2021/10/29-13:02:56-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: 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: 2021/10/29-13:02:56-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: 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 lh 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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... nquads=1572865, nvertices=438 ERROR: MRISread: file '../surf/lh.sphere' has many more faces than vertices! Probably trying to use a scalar data file as a surface! 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 lh -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: 2021/11/12-02:58:52-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 lh 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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... nquads=1572865, nvertices=438 ERROR: MRISread: file '../surf/lh.sphere' has many more faces than vertices! Probably trying to use a scalar data file as a surface! 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 10:08:56 EST 2021 /data/bids/derivatives/fmriprep-20.2.6/freesurfer/sub-8004 /opt/freesurfer/bin/recon-all -autorecon-hemi lh -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 40675816 147184244 6625892 8807868 148181684 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: 2021/11/12-15:08:56-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: 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 lh 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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... nquads=1572865, nvertices=438 ERROR: MRISread: file '../surf/lh.sphere' has many more faces than vertices! Probably trying to use a scalar data file as a surface! 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 lh -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 41312524 146629384 6752712 8726020 147403332 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 lh 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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... nquads=1572865, nvertices=438 ERROR: MRISread: file '../surf/lh.sphere' has many more faces than vertices! Probably trying to use a scalar data file as a surface! 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 12:34:43 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 lh -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 23181292 164444048 6880976 9052056 165464692 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 lh 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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... nquads=1572865, nvertices=438 ERROR: MRISread: file '../surf/lh.sphere' has many more faces than vertices! Probably trying to use a scalar data file as a surface! 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 lh -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 lh 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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /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.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... nquads=1572865, nvertices=438 ERROR: MRISread: file '../surf/lh.sphere' has many more faces than vertices! Probably trying to use a scalar data file as a surface! 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