Mon May 23 19:21:27 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce /fmri/apps/freesurfer-5.3.0/bin/recon-all -i origfinal.mgz -subjid Luce -autorecon1 -no-wsgcaatlas -wsthresh 30 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gbw-d-l0047 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257145 maxlocks unlimited maxsignal 257145 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880792 11838772 28866072 306512 25175948 53066292 Swap: 67108860 0 67108860 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/05/23-17:21:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-109-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce mri_convert /data/local/alessia/Luce_segmentation/MPRAGE_04iso/origfinal.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig/001.mgz mri_convert /data/local/alessia/Luce_segmentation/MPRAGE_04iso/origfinal.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/local/alessia/Luce_segmentation/MPRAGE_04iso/origfinal.mgz... TR=2700.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 23 19:21:49 CEST 2022 Found 1 runs /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig/001.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/rawavg.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce mri_convert /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/rawavg.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig.mgz --conform mri_convert /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/rawavg.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/rawavg.mgz... TR=2700.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig.mgz... mri_add_xform_to_header -c /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/transforms/talairach.xfm /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig.mgz /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 23 19:22:02 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon May 23 19:24:11 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2315, pval=0.0169 >= threshold=0.0050) awk -f /fmri/apps/freesurfer-5.3.0/bin/extract_talairach_avi_QA.awk /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/transforms/talairach_avi.log tal_QC_AZS /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/transforms/talairach_avi.log TalAviQA: 0.96256 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Mon May 23 19:24:11 CEST 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri /fmri/apps/freesurfer-5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gbw-d-l0047 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon May 23 19:24:11 CEST 2022 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.21977 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21977/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21977/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2700.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.21977/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon May 23 19:24:14 CEST 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.21977/nu0.mnc ./tmp.mri_nu_correct.mni.21977/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.21977/0/ [u0146233@gbw-d-l0047:/mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/] [2022-05-23 19:24:14] running: /fmri/apps/freesurfer-5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.21977/0/ ./tmp.mri_nu_correct.mni.21977/nu0.mnc ./tmp.mri_nu_correct.mni.21977/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000996294 [u0146233@gbw-d-l0047:/mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/] [2022-05-23 19:25:02] running: /fmri/apps/freesurfer-5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.21977/nu0.mnc ./tmp.mri_nu_correct.mni.21977/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon May 23 19:25:09 CEST 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.21977/nu1.mnc ./tmp.mri_nu_correct.mni.21977/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.21977/1/ [u0146233@gbw-d-l0047:/mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/] [2022-05-23 19:25:09] running: /fmri/apps/freesurfer-5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.21977/1/ ./tmp.mri_nu_correct.mni.21977/nu1.mnc ./tmp.mri_nu_correct.mni.21977/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 38 CV of field change: 0.00098511 [u0146233@gbw-d-l0047:/mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/] [2022-05-23 19:26:03] running: /fmri/apps/freesurfer-5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.21977/nu1.mnc ./tmp.mri_nu_correct.mni.21977/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.21977/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.21977/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.21977/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.21977/ones.mgz sysname Linux hostname gbw-d-l0047 machine x86_64 user u0146233 input ./tmp.mri_nu_correct.mni.21977/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.21977/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21977/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.21977/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21977/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21977/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.21977/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21977/input.mean.dat sysname Linux hostname gbw-d-l0047 machine x86_64 user u0146233 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.21977/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.21977/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21977/ones.mgz --i ./tmp.mri_nu_correct.mni.21977/nu2.mnc --sum ./tmp.mri_nu_correct.mni.21977/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21977/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21977/ones.mgz --i ./tmp.mri_nu_correct.mni.21977/nu2.mnc --sum ./tmp.mri_nu_correct.mni.21977/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21977/output.mean.dat sysname Linux hostname gbw-d-l0047 machine x86_64 user u0146233 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.21977/ones.mgz Loading ./tmp.mri_nu_correct.mni.21977/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.21977/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.21977/nu2.mnc ./tmp.mri_nu_correct.mni.21977/nu2.mnc mul .85970103146267727527 Saving result to './tmp.mri_nu_correct.mni.21977/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.21977/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.21977/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.21977/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (24, 106) to ( 3, 110) Mon May 23 19:26:46 CEST 2022 mri_nu_correct.mni done mri_add_xform_to_header -c /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon May 23 19:26:47 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.956 0.006 -0.016 34.841; 0.030 1.023 -0.316 67.024; 0.019 -0.310 1.544 -130.448; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 9 Starting OpenSpline(): npoints = 9 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 91 gm peak at 67 (67), valley at 56 (56) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 91 gm peak at 66 (66), valley at 55 (55) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 21 seconds. #-------------------------------------------- #@# Skull Stripping Mon May 23 19:29:08 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_watershed -T1 -h 30 T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Preflooding height manually specified ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz *************************WATERSHED************************** Sorting... T1-weighted MRI image Count how many 110 voxels are present : 64605 Find the largest 110-component... heap usage = 728348 Kbytes. current max segment has 9068 voxels heap usage = 728540 Kbytes. current max segment has 9068 voxels heap usage = 728740 Kbytes. current max segment has 9068 voxels heap usage = 729080 Kbytes. current max segment has 9068 voxels heap usage = 729428 Kbytes. current max segment has 9068 voxels heap usage = 729780 Kbytes. current max segment has 9068 voxels removing small segments (less than 1 percent of maxarea). heap usage = 728804 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 9068 voxels first estimation of the COG coord: x=124 y=135 z=98 r=104 first estimation of the main basin volume: 4828991 voxels global maximum in x=175, y=132, z=76, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 30 percent done. Analyze... main basin size= 1694759 voxels, voxel volume =1.000 = 1694759 mmm3 = 1694.759 cm3 done. PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=125, z=103, r=11289 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45278 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 8, 53, 71 after analyzing : 4, 38, 53, 46 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...67 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 72.414, std = 10.710 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 7.11, sigma = 11.23 after rotation: sse = 7.11, sigma = 11.23 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.32, its var is 14.51 before Erosion-Dilatation 8.73% of inacurate vertices after Erosion-Dilatation 14.73% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mri_strip_skull: done peeling brain Brain Size = 1813869 voxels, voxel volume = 1.000 mm3 = 1813869 mmm3 = 1813.869 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ Started at Mon May 23 19:21:27 CEST 2022 Ended at Mon May 23 19:29:30 CEST 2022 #@#%# recon-all-run-time-hours 0.134 recon-all -s Luce finished without error at Mon May 23 19:29:31 CEST 2022 New invocation of recon-all Wed Jul 20 11:48:59 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce /fmri/apps/freesurfer-5.3.0/bin/recon-all -s Luce -autorecon2-inflate1 -noaseg -cc-crs 128 108 129 -pons-crs 128 143 105 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gbw-d-l0047 5.4.0-122-generic #138~18.04.1-Ubuntu SMP Fri Jun 24 14:14:03 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257143 maxlocks unlimited maxsignal 257143 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880800 9243336 45856000 267284 10781464 55700960 Swap: 67108860 0 67108860 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:48:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:48:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:01-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:01-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:01-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:01-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-09:49:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Wed Jul 20 11:49:08 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_normalize brainmask.mgz brain.mgz reading from brainmask.mgz... normalizing image... talairach transform 0.956 0.006 -0.016 34.841; 0.030 1.023 -0.316 67.024; 0.019 -0.310 1.544 -130.448; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 6 Starting OpenSpline(): npoints = 6 mghWrite(brain.mgz, -1): could not open file building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 100 gm peak at 69 (69), valley at 42 (42) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 100 gm peak at 70 (70), valley at 42 (42) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 26 seconds. #-------------------------------------------- #@# Mask BFS Wed Jul 20 11:51:34 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1658623 voxels in mask (pct= 9.89) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jul 20 11:51:37 CEST 2022 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.2 +- 7.2 [80.0 --> 125.0] GM (74.0) : 72.6 +- 10.7 [30.0 --> 96.0] setting bottom of white matter range to 83.3 setting top of gray matter range to 94.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 12822 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4646 filled 53 bright non-wm voxels segmented. 11012 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... mri_pretess wm.seg.mgz wm brain.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 34 found - 34 modified | TOTAL: 34 pass 2 (xy+): 0 found - 34 modified | TOTAL: 34 pass 1 (xy-): 54 found - 54 modified | TOTAL: 88 pass 2 (xy-): 0 found - 54 modified | TOTAL: 88 pass 1 (yz+): 49 found - 49 modified | TOTAL: 137 pass 2 (yz+): 0 found - 49 modified | TOTAL: 137 pass 1 (yz-): 56 found - 56 modified | TOTAL: 193 pass 2 (yz-): 0 found - 56 modified | TOTAL: 193 pass 1 (xz+): 71 found - 71 modified | TOTAL: 264 pass 2 (xz+): 0 found - 71 modified | TOTAL: 264 pass 1 (xz-): 73 found - 73 modified | TOTAL: 337 pass 2 (xz-): 0 found - 73 modified | TOTAL: 337 Iteration Number : 1 pass 1 (+++): 293 found - 293 modified | TOTAL: 293 pass 2 (+++): 0 found - 293 modified | TOTAL: 293 pass 1 (+++): 185 found - 185 modified | TOTAL: 478 pass 2 (+++): 0 found - 185 modified | TOTAL: 478 pass 1 (+++): 244 found - 244 modified | TOTAL: 722 pass 2 (+++): 0 found - 244 modified | TOTAL: 722 pass 1 (+++): 200 found - 200 modified | TOTAL: 922 pass 2 (+++): 0 found - 200 modified | TOTAL: 922 Iteration Number : 1 pass 1 (++): 530 found - 530 modified | TOTAL: 530 pass 2 (++): 0 found - 530 modified | TOTAL: 530 pass 1 (+-): 643 found - 643 modified | TOTAL: 1173 pass 2 (+-): 3 found - 646 modified | TOTAL: 1176 pass 3 (+-): 0 found - 646 modified | TOTAL: 1176 pass 1 (--): 490 found - 490 modified | TOTAL: 1666 pass 2 (--): 1 found - 491 modified | TOTAL: 1667 pass 3 (--): 0 found - 491 modified | TOTAL: 1667 pass 1 (-+): 605 found - 605 modified | TOTAL: 2272 pass 2 (-+): 0 found - 605 modified | TOTAL: 2272 Iteration Number : 2 pass 1 (xy+): 91 found - 91 modified | TOTAL: 91 pass 2 (xy+): 0 found - 91 modified | TOTAL: 91 pass 1 (xy-): 76 found - 76 modified | TOTAL: 167 pass 2 (xy-): 0 found - 76 modified | TOTAL: 167 pass 1 (yz+): 104 found - 104 modified | TOTAL: 271 pass 2 (yz+): 0 found - 104 modified | TOTAL: 271 pass 1 (yz-): 98 found - 98 modified | TOTAL: 369 pass 2 (yz-): 0 found - 98 modified | TOTAL: 369 pass 1 (xz+): 97 found - 97 modified | TOTAL: 466 pass 2 (xz+): 0 found - 97 modified | TOTAL: 466 pass 1 (xz-): 79 found - 79 modified | TOTAL: 545 pass 2 (xz-): 0 found - 79 modified | TOTAL: 545 Iteration Number : 2 pass 1 (+++): 44 found - 44 modified | TOTAL: 44 pass 2 (+++): 0 found - 44 modified | TOTAL: 44 pass 1 (+++): 33 found - 33 modified | TOTAL: 77 pass 2 (+++): 0 found - 33 modified | TOTAL: 77 pass 1 (+++): 34 found - 34 modified | TOTAL: 111 pass 2 (+++): 0 found - 34 modified | TOTAL: 111 pass 1 (+++): 39 found - 39 modified | TOTAL: 150 pass 2 (+++): 0 found - 39 modified | TOTAL: 150 Iteration Number : 2 pass 1 (++): 47 found - 47 modified | TOTAL: 47 pass 2 (++): 0 found - 47 modified | TOTAL: 47 pass 1 (+-): 41 found - 41 modified | TOTAL: 88 pass 2 (+-): 2 found - 43 modified | TOTAL: 90 pass 3 (+-): 0 found - 43 modified | TOTAL: 90 pass 1 (--): 62 found - 62 modified | TOTAL: 152 pass 2 (--): 0 found - 62 modified | TOTAL: 152 pass 1 (-+): 48 found - 48 modified | TOTAL: 200 pass 2 (-+): 0 found - 48 modified | TOTAL: 200 Iteration Number : 3 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 10 found - 10 modified | TOTAL: 25 pass 2 (xy-): 0 found - 10 modified | TOTAL: 25 pass 1 (yz+): 18 found - 18 modified | TOTAL: 43 pass 2 (yz+): 0 found - 18 modified | TOTAL: 43 pass 1 (yz-): 13 found - 13 modified | TOTAL: 56 pass 2 (yz-): 0 found - 13 modified | TOTAL: 56 pass 1 (xz+): 20 found - 20 modified | TOTAL: 76 pass 2 (xz+): 0 found - 20 modified | TOTAL: 76 pass 1 (xz-): 7 found - 7 modified | TOTAL: 83 pass 2 (xz-): 0 found - 7 modified | TOTAL: 83 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 3 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 7 found - 7 modified | TOTAL: 12 pass 2 (+-): 0 found - 7 modified | TOTAL: 12 pass 1 (--): 10 found - 10 modified | TOTAL: 22 pass 2 (--): 0 found - 10 modified | TOTAL: 22 pass 1 (-+): 8 found - 8 modified | TOTAL: 30 pass 2 (-+): 0 found - 8 modified | TOTAL: 30 Iteration Number : 4 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 1 found - 1 modified | TOTAL: 10 pass 2 (yz-): 0 found - 1 modified | TOTAL: 10 pass 1 (xz+): 0 found - 0 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 4 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 : 4 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 5 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 : 5 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 : 5 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 = 4558 (out of 465570: 0.979015) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Jul 20 11:53:34 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_fill -a ../scripts/ponscc.cut.log -Pv 128 143 105 -Cv 128 108 129 wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position (128, 143, 105) as pons seed point using voxel position (128, 108, 129) as corpus callosum seed point reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. Looking for area (min, max) = (350, 1400) area[0] = 389 (min = 350, max = 1400), aspect = 0.30 (min = 0.10, max = 0.75) no need to search using seed (128, 108, 129), TAL = (-34.7, -39.2, 89.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (-34.75, -39.20, 89.56) Using the seed to calculate the cutting plane Looking for area (min, max) = (350, 790) area[0] = 4616 (min = 350, max = 790), aspect = 0.95 (min = 0.60, max = 1.20) need search nearby using seed (128, 143, 105), TAL = (-34.7, -63.2, 54.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (-34.75, -39.20, 89.56) Using voxel pons seed point, calculated talairach pons position (-34.75, -63.20, 54.56) find_cutting_plane:seed point not in structure! Searching neighborhood... done. filling left hemisphere... filling volume: pass 1 of 3...total of 323193 voxels filled... filling volume: pass 2 of 3...total of 16385690 voxels filled... filling volume: pass 3 of 3...total of 324969 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 323193 voxels filled... filling volume: pass 2 of 3...total of 16385690 voxels filled... filling volume: pass 3 of 3...total of 324969 voxels filled...done. filling degenerate left hemisphere surface locations... 977 voxels filled 53 voxels filled 7 voxels filled 3 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 977 voxels filled 53 voxels filled 7 voxels filled 3 voxels filled 0 voxels filled refilling left hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16384570 voxels filled... filling volume: pass 3 of 3...total of 326089 voxels filled...done. refilling right hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16384570 voxels filled... filling volume: pass 3 of 3...total of 326089 voxels filled...done. combining hemispheres... using variable coefficient diffusion to correct hemispheric overlap... 26: 325692 ambiguous voxels remaining 9: 41383 ambiguous voxels remaining 8: 20226 ambiguous voxels remaining 7: 9403 ambiguous voxels remaining 6: 4705 ambiguous voxels remaining 5: 2910 ambiguous voxels remaining 4: 1350 ambiguous voxels remaining 3: 634 ambiguous voxels remaining 2: 235 ambiguous voxels remaining 1: 0 ambiguous voxels remaining writing output to filled.mgz... filling took 0.7 minutes seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(-16.75, -39.20, 89.56) SRC: (110.00, 108.00, 129.00) search lh wm seed point around talairach space (-52.75, -39.20, 89.56), SRC: (146.00, 108.00, 129.00) #-------------------------------------------- #@# Tessellate lh Wed Jul 20 11:54:17 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 3 found - 3 modified | TOTAL: 3 pass 2 (yz-): 0 found - 3 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 0 found - 0 modified | TOTAL: 10 pass 1 (+++): 1 found - 1 modified | TOTAL: 11 pass 2 (+++): 0 found - 1 modified | TOTAL: 11 pass 1 (+++): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 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+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 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 : 4 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 : 5 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 : 5 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 : 5 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 = 30 (out of 160109: 0.018737) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 21 vertices, 30 faces slice 30: 2263 vertices, 2393 faces slice 40: 7897 vertices, 8136 faces slice 50: 14908 vertices, 15292 faces slice 60: 21981 vertices, 22333 faces slice 70: 28290 vertices, 28673 faces slice 80: 35362 vertices, 35730 faces slice 90: 44029 vertices, 44501 faces slice 100: 53260 vertices, 53769 faces slice 110: 63656 vertices, 64305 faces slice 120: 74858 vertices, 75660 faces slice 130: 84882 vertices, 85596 faces slice 140: 93257 vertices, 93998 faces slice 150: 99674 vertices, 100335 faces slice 160: 105347 vertices, 106010 faces slice 170: 109954 vertices, 110555 faces slice 180: 112788 vertices, 113361 faces slice 190: 114787 vertices, 115329 faces slice 200: 115790 vertices, 116309 faces slice 210: 116034 vertices, 116530 faces slice 220: 116034 vertices, 116530 faces slice 230: 116034 vertices, 116530 faces slice 240: 116034 vertices, 116530 faces slice 250: 116034 vertices, 116530 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 116034 voxel in cpt #1: X=-496 [v=116034,e=349590,f=233060] located at (-28.112890, -25.948576, 12.819165) For the whole surface: X=-496 [v=116034,e=349590,f=233060] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jul 20 11:54:24 CEST 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Jul 20 11:54:27 CEST 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 45.2 mm, total surface area = 62594 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.122 (target=0.015) step 005: RMS=0.098 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.085 (target=0.015) step 020: RMS=0.083 (target=0.015) step 025: RMS=0.080 (target=0.015) step 030: RMS=0.079 (target=0.015) step 035: RMS=0.079 (target=0.015) step 040: RMS=0.079 (target=0.015) step 045: RMS=0.079 (target=0.015) step 050: RMS=0.079 (target=0.015) step 055: RMS=0.080 (target=0.015) step 060: RMS=0.080 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Tessellate rh Wed Jul 20 11:54:52 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 2 found - 2 modified | TOTAL: 3 pass 2 (xz-): 0 found - 2 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 1 found - 1 modified | TOTAL: 13 pass 2 (+++): 0 found - 1 modified | TOTAL: 13 pass 1 (+++): 1 found - 1 modified | TOTAL: 14 pass 2 (+++): 0 found - 1 modified | TOTAL: 14 pass 1 (+++): 0 found - 0 modified | TOTAL: 14 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 25 (out of 166036: 0.015057) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 100 vertices, 122 faces slice 30: 3138 vertices, 3320 faces slice 40: 9864 vertices, 10164 faces slice 50: 18507 vertices, 18885 faces slice 60: 24976 vertices, 25322 faces slice 70: 31686 vertices, 32059 faces slice 80: 38870 vertices, 39272 faces slice 90: 47793 vertices, 48275 faces slice 100: 57015 vertices, 57547 faces slice 110: 67293 vertices, 67968 faces slice 120: 78166 vertices, 78941 faces slice 130: 87470 vertices, 88236 faces slice 140: 95432 vertices, 96212 faces slice 150: 101381 vertices, 102086 faces slice 160: 106868 vertices, 107586 faces slice 170: 111392 vertices, 112056 faces slice 180: 114105 vertices, 114742 faces slice 190: 116137 vertices, 116739 faces slice 200: 117321 vertices, 117889 faces slice 210: 117568 vertices, 118108 faces slice 220: 117568 vertices, 118108 faces slice 230: 117568 vertices, 118108 faces slice 240: 117568 vertices, 118108 faces slice 250: 117568 vertices, 118108 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 117538 voxel in cpt #1: X=-542 [v=117538,e=354240,f=236160] located at (29.170124, -28.398390, 11.751144) 30 voxel in cpt #2: X=2 [v=30,e=84,f=56] located at (22.299999, -98.099998, -11.000000) For the whole surface: X=-540 [v=117568,e=354324,f=236216] 2 components have been found keeping component #1 with 117538 vertices done #-------------------------------------------- #@# Smooth1 rh Wed Jul 20 11:54:58 CEST 2022 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Jul 20 11:55:01 CEST 2022 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 45.7 mm, total surface area = 62992 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.127 (target=0.015) step 005: RMS=0.104 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.091 (target=0.015) step 020: RMS=0.088 (target=0.015) step 025: RMS=0.087 (target=0.015) step 030: RMS=0.085 (target=0.015) step 035: RMS=0.085 (target=0.015) step 040: RMS=0.085 (target=0.015) step 045: RMS=0.084 (target=0.015) step 050: RMS=0.084 (target=0.015) step 055: RMS=0.084 (target=0.015) step 060: RMS=0.084 (target=0.015) inflation complete. Not saving sulc #------------------------------------------ Started at Wed Jul 20 11:48:58 CEST 2022 Ended at Wed Jul 20 11:55:26 CEST 2022 #@#%# recon-all-run-time-hours 0.108 recon-all -s Luce finished without error at Wed Jul 20 11:55:26 CEST 2022 New invocation of recon-all Wed Jul 20 13:06:25 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce /fmri/apps/freesurfer-5.3.0/bin/recon-all -s Luce -autorecon2-inflate1 -noaseg -cc-crs 128 108 129 -pons-crs 128, 184, 82 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gbw-d-l0047 5.4.0-122-generic #138~18.04.1-Ubuntu SMP Fri Jun 24 14:14:03 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257143 maxlocks unlimited maxsignal 257143 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880800 9138916 45743612 268484 10998272 55804184 Swap: 67108860 0 67108860 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/07/20-11:06:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-122-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Wed Jul 20 13:06:29 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_normalize brainmask.mgz brain.mgz reading from brainmask.mgz... normalizing image... talairach transform 0.956 0.006 -0.016 34.841; 0.030 1.023 -0.316 67.024; 0.019 -0.310 1.544 -130.448; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 6 Starting OpenSpline(): npoints = 6 mghWrite(brain.mgz, -1): could not open file building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 100 gm peak at 69 (69), valley at 42 (42) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 100 gm peak at 70 (70), valley at 42 (42) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 24 seconds. #-------------------------------------------- #@# Mask BFS Wed Jul 20 13:08:54 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1658623 voxels in mask (pct= 9.89) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jul 20 13:08:55 CEST 2022 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname gbw-d-l0047 machine x86_64 user u0146233 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname gbw-d-l0047 machine x86_64 user u0146233 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.2 +- 7.2 [80.0 --> 125.0] GM (74.0) : 72.6 +- 10.7 [30.0 --> 96.0] setting bottom of white matter range to 83.3 setting top of gray matter range to 94.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 12822 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4646 filled 53 bright non-wm voxels segmented. 11012 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... mri_pretess -keep wm.seg.mgz wm brain.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 34 found - 34 modified | TOTAL: 34 pass 2 (xy+): 0 found - 34 modified | TOTAL: 34 pass 1 (xy-): 54 found - 54 modified | TOTAL: 88 pass 2 (xy-): 0 found - 54 modified | TOTAL: 88 pass 1 (yz+): 49 found - 49 modified | TOTAL: 137 pass 2 (yz+): 0 found - 49 modified | TOTAL: 137 pass 1 (yz-): 56 found - 56 modified | TOTAL: 193 pass 2 (yz-): 0 found - 56 modified | TOTAL: 193 pass 1 (xz+): 71 found - 71 modified | TOTAL: 264 pass 2 (xz+): 0 found - 71 modified | TOTAL: 264 pass 1 (xz-): 73 found - 73 modified | TOTAL: 337 pass 2 (xz-): 0 found - 73 modified | TOTAL: 337 Iteration Number : 1 pass 1 (+++): 293 found - 293 modified | TOTAL: 293 pass 2 (+++): 0 found - 293 modified | TOTAL: 293 pass 1 (+++): 185 found - 185 modified | TOTAL: 478 pass 2 (+++): 0 found - 185 modified | TOTAL: 478 pass 1 (+++): 244 found - 244 modified | TOTAL: 722 pass 2 (+++): 0 found - 244 modified | TOTAL: 722 pass 1 (+++): 200 found - 200 modified | TOTAL: 922 pass 2 (+++): 0 found - 200 modified | TOTAL: 922 Iteration Number : 1 pass 1 (++): 530 found - 530 modified | TOTAL: 530 pass 2 (++): 0 found - 530 modified | TOTAL: 530 pass 1 (+-): 643 found - 643 modified | TOTAL: 1173 pass 2 (+-): 3 found - 646 modified | TOTAL: 1176 pass 3 (+-): 0 found - 646 modified | TOTAL: 1176 pass 1 (--): 490 found - 490 modified | TOTAL: 1666 pass 2 (--): 1 found - 491 modified | TOTAL: 1667 pass 3 (--): 0 found - 491 modified | TOTAL: 1667 pass 1 (-+): 605 found - 605 modified | TOTAL: 2272 pass 2 (-+): 0 found - 605 modified | TOTAL: 2272 Iteration Number : 2 pass 1 (xy+): 91 found - 91 modified | TOTAL: 91 pass 2 (xy+): 0 found - 91 modified | TOTAL: 91 pass 1 (xy-): 76 found - 76 modified | TOTAL: 167 pass 2 (xy-): 0 found - 76 modified | TOTAL: 167 pass 1 (yz+): 104 found - 104 modified | TOTAL: 271 pass 2 (yz+): 0 found - 104 modified | TOTAL: 271 pass 1 (yz-): 98 found - 98 modified | TOTAL: 369 pass 2 (yz-): 0 found - 98 modified | TOTAL: 369 pass 1 (xz+): 97 found - 97 modified | TOTAL: 466 pass 2 (xz+): 0 found - 97 modified | TOTAL: 466 pass 1 (xz-): 79 found - 79 modified | TOTAL: 545 pass 2 (xz-): 0 found - 79 modified | TOTAL: 545 Iteration Number : 2 pass 1 (+++): 44 found - 44 modified | TOTAL: 44 pass 2 (+++): 0 found - 44 modified | TOTAL: 44 pass 1 (+++): 33 found - 33 modified | TOTAL: 77 pass 2 (+++): 0 found - 33 modified | TOTAL: 77 pass 1 (+++): 34 found - 34 modified | TOTAL: 111 pass 2 (+++): 0 found - 34 modified | TOTAL: 111 pass 1 (+++): 39 found - 39 modified | TOTAL: 150 pass 2 (+++): 0 found - 39 modified | TOTAL: 150 Iteration Number : 2 pass 1 (++): 47 found - 47 modified | TOTAL: 47 pass 2 (++): 0 found - 47 modified | TOTAL: 47 pass 1 (+-): 41 found - 41 modified | TOTAL: 88 pass 2 (+-): 2 found - 43 modified | TOTAL: 90 pass 3 (+-): 0 found - 43 modified | TOTAL: 90 pass 1 (--): 62 found - 62 modified | TOTAL: 152 pass 2 (--): 0 found - 62 modified | TOTAL: 152 pass 1 (-+): 48 found - 48 modified | TOTAL: 200 pass 2 (-+): 0 found - 48 modified | TOTAL: 200 Iteration Number : 3 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 10 found - 10 modified | TOTAL: 25 pass 2 (xy-): 0 found - 10 modified | TOTAL: 25 pass 1 (yz+): 18 found - 18 modified | TOTAL: 43 pass 2 (yz+): 0 found - 18 modified | TOTAL: 43 pass 1 (yz-): 13 found - 13 modified | TOTAL: 56 pass 2 (yz-): 0 found - 13 modified | TOTAL: 56 pass 1 (xz+): 20 found - 20 modified | TOTAL: 76 pass 2 (xz+): 0 found - 20 modified | TOTAL: 76 pass 1 (xz-): 7 found - 7 modified | TOTAL: 83 pass 2 (xz-): 0 found - 7 modified | TOTAL: 83 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 3 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 7 found - 7 modified | TOTAL: 12 pass 2 (+-): 0 found - 7 modified | TOTAL: 12 pass 1 (--): 10 found - 10 modified | TOTAL: 22 pass 2 (--): 0 found - 10 modified | TOTAL: 22 pass 1 (-+): 8 found - 8 modified | TOTAL: 30 pass 2 (-+): 0 found - 8 modified | TOTAL: 30 Iteration Number : 4 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 1 found - 1 modified | TOTAL: 10 pass 2 (yz-): 0 found - 1 modified | TOTAL: 10 pass 1 (xz+): 0 found - 0 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 4 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 : 4 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 5 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 : 5 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 : 5 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 = 4558 (out of 465570: 0.979015) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Wed Jul 20 13:10:59 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_fill -a ../scripts/ponscc.cut.log -Pv 128, 184, 82 -Cv 128 108 129 wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position (128, 184, 82) as pons seed point using voxel position (128, 108, 129) as corpus callosum seed point reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. Looking for area (min, max) = (350, 1400) area[0] = 389 (min = 350, max = 1400), aspect = 0.30 (min = 0.10, max = 0.75) no need to search using seed (128, 108, 129), TAL = (-34.7, -39.2, 89.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (-34.75, -39.20, 89.56) Using the seed to calculate the cutting plane Looking for area (min, max) = (350, 790) area[0] = 258 (min = 350, max = 790), aspect = 1.36 (min = 0.60, max = 1.20) need search nearby using seed (128, 184, 82), TAL = (-34.7, -86.2, 13.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (-34.75, -39.20, 89.56) Using voxel pons seed point, calculated talairach pons position (-34.75, -86.20, 13.56) find_cutting_plane:seed point not in structure! Searching neighborhood... done. filling left hemisphere... filling volume: pass 1 of 3...total of 460476 voxels filled... filling volume: pass 2 of 3...total of 16247095 voxels filled... filling volume: pass 3 of 3...total of 463564 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 460476 voxels filled... filling volume: pass 2 of 3...total of 16247095 voxels filled... filling volume: pass 3 of 3...total of 463564 voxels filled...done. filling degenerate left hemisphere surface locations... 1894 voxels filled 112 voxels filled 18 voxels filled 5 voxels filled 1 voxels filled 1 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 1894 voxels filled 112 voxels filled 18 voxels filled 5 voxels filled 1 voxels filled 1 voxels filled 0 voxels filled refilling left hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16244885 voxels filled... filling volume: pass 3 of 3...total of 465774 voxels filled...done. refilling right hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16244885 voxels filled... filling volume: pass 3 of 3...total of 465774 voxels filled...done. combining hemispheres... using variable coefficient diffusion to correct hemispheric overlap... 26: 465377 ambiguous voxels remaining 9: 147465 ambiguous voxels remaining 8: 53096 ambiguous voxels remaining 7: 30876 ambiguous voxels remaining 6: 12673 ambiguous voxels remaining 5: 5154 ambiguous voxels remaining 4: 2461 ambiguous voxels remaining 3: 1010 ambiguous voxels remaining 2: 305 ambiguous voxels remaining 1: 0 ambiguous voxels remaining writing output to filled.mgz... filling took 0.8 minutes seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(-16.75, -39.20, 89.56) SRC: (110.00, 108.00, 129.00) search lh wm seed point around talairach space (-52.75, -39.20, 89.56), SRC: (146.00, 108.00, 129.00) #-------------------------------------------- #@# Tessellate lh Wed Jul 20 13:11:45 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 255 ../mri/brain.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-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 11 found - 11 modified | TOTAL: 16 pass 2 (yz-): 0 found - 11 modified | TOTAL: 16 pass 1 (xz+): 3 found - 3 modified | TOTAL: 19 pass 2 (xz+): 0 found - 3 modified | TOTAL: 19 pass 1 (xz-): 4 found - 4 modified | TOTAL: 23 pass 2 (xz-): 0 found - 4 modified | TOTAL: 23 Iteration Number : 1 pass 1 (+++): 14 found - 14 modified | TOTAL: 14 pass 2 (+++): 0 found - 14 modified | TOTAL: 14 pass 1 (+++): 0 found - 0 modified | TOTAL: 14 pass 1 (+++): 1 found - 1 modified | TOTAL: 15 pass 2 (+++): 0 found - 1 modified | TOTAL: 15 pass 1 (+++): 0 found - 0 modified | TOTAL: 15 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 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+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 4 found - 4 modified | TOTAL: 8 pass 2 (xz+): 0 found - 4 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 2 found - 2 modified | TOTAL: 6 pass 2 (-+): 0 found - 2 modified | TOTAL: 6 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 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 : 4 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 : 5 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 : 5 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 : 5 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 = 58 (out of 236512: 0.024523) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 21 vertices, 30 faces slice 30: 2674 vertices, 2848 faces slice 40: 11063 vertices, 11481 faces slice 50: 26176 vertices, 27039 faces slice 60: 46549 vertices, 47511 faces slice 70: 66536 vertices, 67640 faces slice 80: 85867 vertices, 87049 faces slice 90: 103458 vertices, 104631 faces slice 100: 119500 vertices, 120777 faces slice 110: 136110 vertices, 137576 faces slice 120: 151511 vertices, 153092 faces slice 130: 163885 vertices, 165330 faces slice 140: 174045 vertices, 175515 faces slice 150: 181868 vertices, 183223 faces slice 160: 187817 vertices, 189150 faces slice 170: 192424 vertices, 193695 faces slice 180: 195258 vertices, 196501 faces slice 190: 197257 vertices, 198469 faces slice 200: 198260 vertices, 199449 faces slice 210: 198504 vertices, 199670 faces slice 220: 198504 vertices, 199670 faces slice 230: 198504 vertices, 199670 faces slice 240: 198504 vertices, 199670 faces slice 250: 198504 vertices, 199670 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 198488 voxel in cpt #1: X=-1168 [v=198488,e=598968,f=399312] located at (-23.908922, -36.872288, -4.399520) 16 voxel in cpt #2: X=2 [v=16,e=42,f=28] located at (-10.000000, -36.375000, -29.625000) For the whole surface: X=-1166 [v=198504,e=599010,f=399340] 2 components have been found keeping component #1 with 198488 vertices done #-------------------------------------------- #@# Smooth1 lh Wed Jul 20 13:11:54 CEST 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Jul 20 13:11:59 CEST 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 49.6 mm, total surface area = 100707 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.138 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.104 (target=0.015) step 015: RMS=0.100 (target=0.015) step 020: RMS=0.097 (target=0.015) step 025: RMS=0.094 (target=0.015) step 030: RMS=0.093 (target=0.015) step 035: RMS=0.093 (target=0.015) step 040: RMS=0.092 (target=0.015) step 045: RMS=0.092 (target=0.015) step 050: RMS=0.092 (target=0.015) step 055: RMS=0.091 (target=0.015) step 060: RMS=0.091 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Tessellate rh Wed Jul 20 13:12:40 CEST 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 1 found - 1 modified | TOTAL: 6 pass 2 (xy-): 0 found - 1 modified | TOTAL: 6 pass 1 (yz+): 4 found - 4 modified | TOTAL: 10 pass 2 (yz+): 0 found - 4 modified | TOTAL: 10 pass 1 (yz-): 7 found - 7 modified | TOTAL: 17 pass 2 (yz-): 0 found - 7 modified | TOTAL: 17 pass 1 (xz+): 3 found - 3 modified | TOTAL: 20 pass 2 (xz+): 0 found - 3 modified | TOTAL: 20 pass 1 (xz-): 5 found - 5 modified | TOTAL: 25 pass 2 (xz-): 0 found - 5 modified | TOTAL: 25 Iteration Number : 1 pass 1 (+++): 24 found - 24 modified | TOTAL: 24 pass 2 (+++): 0 found - 24 modified | TOTAL: 24 pass 1 (+++): 1 found - 1 modified | TOTAL: 25 pass 2 (+++): 0 found - 1 modified | TOTAL: 25 pass 1 (+++): 3 found - 3 modified | TOTAL: 28 pass 2 (+++): 0 found - 3 modified | TOTAL: 28 pass 1 (+++): 0 found - 0 modified | TOTAL: 28 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 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 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 0 found - 0 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 1 found - 1 modified | TOTAL: 6 pass 2 (-+): 0 found - 1 modified | TOTAL: 6 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 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 : 4 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 : 4 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 = 76 (out of 229397: 0.033130) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 103 vertices, 126 faces slice 30: 3382 vertices, 3586 faces slice 40: 11791 vertices, 12282 faces slice 50: 27253 vertices, 28016 faces slice 60: 43052 vertices, 43929 faces slice 70: 58112 vertices, 59004 faces slice 80: 71846 vertices, 72742 faces slice 90: 86700 vertices, 87696 faces slice 100: 102625 vertices, 103788 faces slice 110: 119252 vertices, 120601 faces slice 120: 134479 vertices, 135859 faces slice 130: 146360 vertices, 147708 faces slice 140: 156603 vertices, 157945 faces slice 150: 163826 vertices, 165048 faces slice 160: 169398 vertices, 170618 faces slice 170: 173922 vertices, 175088 faces slice 180: 176635 vertices, 177774 faces slice 190: 178667 vertices, 179771 faces slice 200: 179851 vertices, 180921 faces slice 210: 180098 vertices, 181140 faces slice 220: 180098 vertices, 181140 faces slice 230: 180098 vertices, 181140 faces slice 240: 180098 vertices, 181140 faces slice 250: 180098 vertices, 181140 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 180068 voxel in cpt #1: X=-1044 [v=180068,e=543336,f=362224] located at (28.188257, -35.248367, -2.709154) 30 voxel in cpt #2: X=2 [v=30,e=84,f=56] located at (22.299999, -98.099998, -11.000000) For the whole surface: X=-1042 [v=180098,e=543420,f=362280] 2 components have been found keeping component #1 with 180068 vertices done #-------------------------------------------- #@# Smooth1 rh Wed Jul 20 13:12:47 CEST 2022 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Jul 20 13:12:52 CEST 2022 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 48.7 mm, total surface area = 92729 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.136 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.102 (target=0.015) step 015: RMS=0.098 (target=0.015) step 020: RMS=0.095 (target=0.015) step 025: RMS=0.093 (target=0.015) step 030: RMS=0.091 (target=0.015) step 035: RMS=0.090 (target=0.015) step 040: RMS=0.089 (target=0.015) step 045: RMS=0.089 (target=0.015) step 050: RMS=0.088 (target=0.015) step 055: RMS=0.088 (target=0.015) step 060: RMS=0.087 (target=0.015) inflation complete. Not saving sulc #------------------------------------------ Started at Wed Jul 20 13:06:24 CEST 2022 Ended at Wed Jul 20 13:13:29 CEST 2022 #@#%# recon-all-run-time-hours 0.118 recon-all -s Luce finished without error at Wed Jul 20 13:13:29 CEST 2022 New invocation of recon-all Mon Nov 14 19:55:05 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce ./recon-allXL -s Luce -autorecon2-wmq -noaseg -cc-crs 128 108 129 -pons-crs 128, 184, 82 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gbw-d-l0047 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257143 maxlocks unlimited maxsignal 257143 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880800 16574496 38025852 435216 11280452 48201864 Swap: 67108860 1036 67107824 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-18:55:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Fill Mon Nov 14 19:55:13 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_fill -a ../scripts/ponscc.cut.log -Pv 128, 184, 82 -Cv 128 108 129 wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position (128, 184, 82) as pons seed point using voxel position (128, 108, 129) as corpus callosum seed point reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. Looking for area (min, max) = (350, 1400) area[0] = 2409 (min = 350, max = 1400), aspect = 0.71 (min = 0.10, max = 0.75) need search nearby using seed (128, 108, 129), TAL = (-34.7, -39.2, 89.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (-34.75, -39.20, 89.56) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (128, 184, 82), TAL = (-34.7, -86.2, 13.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (-34.75, -39.20, 89.56) Using voxel pons seed point, calculated talairach pons position (-34.75, -86.20, 13.56) find_cutting_plane:seed point not in structure! Searching neighborhood... done. filling left hemisphere... filling volume: pass 1 of 3...total of 219117 voxels filled... filling volume: pass 2 of 3...total of 16491322 voxels filled... filling volume: pass 3 of 3...total of 219337 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 216367 voxels filled... filling volume: pass 2 of 3...total of 16493889 voxels filled... filling volume: pass 3 of 3...total of 216770 voxels filled...done. filling degenerate left hemisphere surface locations... 778 voxels filled 3 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 900 voxels filled 7 voxels filled 0 voxels filled refilling left hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16490537 voxels filled... filling volume: pass 3 of 3...total of 220122 voxels filled...done. refilling right hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16492982 voxels filled... filling volume: pass 3 of 3...total of 217677 voxels filled...done. combining hemispheres... writing output to filled.mgz... filling took 0.2 minutes seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(-16.75, -39.20, 89.56) SRC: (110.00, 108.00, 129.00) search lh wm seed point around talairach space (-52.75, -39.20, 89.56), SRC: (146.00, 108.00, 129.00) #-------------------------------------------- #@# Tessellate lh Mon Nov 14 19:55:27 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 3 found - 3 modified | TOTAL: 5 pass 2 (xz+): 0 found - 3 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 2 found - 2 modified | TOTAL: 5 pass 2 (+++): 0 found - 2 modified | TOTAL: 5 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 4 found - 4 modified | TOTAL: 4 pass 2 (--): 1 found - 5 modified | TOTAL: 5 pass 3 (--): 0 found - 5 modified | TOTAL: 5 pass 1 (-+): 0 found - 0 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 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 : 4 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 : 4 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 = 22 (out of 220145: 0.009993) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 941 vertices, 1006 faces slice 40: 5230 vertices, 5370 faces slice 50: 11458 vertices, 11744 faces slice 60: 18263 vertices, 18490 faces slice 70: 25112 vertices, 25393 faces slice 80: 32719 vertices, 32977 faces slice 90: 42217 vertices, 42580 faces slice 100: 52594 vertices, 52924 faces slice 110: 61317 vertices, 61632 faces slice 120: 69539 vertices, 69874 faces slice 130: 77180 vertices, 77478 faces slice 140: 84238 vertices, 84529 faces slice 150: 90444 vertices, 90646 faces slice 160: 95245 vertices, 95428 faces slice 170: 99372 vertices, 99529 faces slice 180: 102491 vertices, 102626 faces slice 190: 104875 vertices, 104972 faces slice 200: 106140 vertices, 106204 faces slice 210: 106586 vertices, 106610 faces slice 220: 106586 vertices, 106610 faces slice 230: 106586 vertices, 106610 faces slice 240: 106586 vertices, 106610 faces slice 250: 106586 vertices, 106610 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 106586 voxel in cpt #1: X=-24 [v=106586,e=319830,f=213220] located at (-31.678738, -25.275534, 9.667865) For the whole surface: X=-24 [v=106586,e=319830,f=213220] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Nov 14 19:55:33 CET 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Nov 14 19:55:36 CET 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 48.0 mm, total surface area = 62194 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.076 (target=0.015) step 005: RMS=0.058 (target=0.015) step 010: RMS=0.045 (target=0.015) step 015: RMS=0.041 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Tessellate rh Mon Nov 14 19:55:58 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 5 found - 5 modified | TOTAL: 7 pass 2 (xz-): 0 found - 5 modified | TOTAL: 7 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 : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 217688: 0.004594) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 1422 vertices, 1511 faces slice 40: 6072 vertices, 6220 faces slice 50: 13257 vertices, 13510 faces slice 60: 19545 vertices, 19774 faces slice 70: 26873 vertices, 27141 faces slice 80: 34482 vertices, 34779 faces slice 90: 44425 vertices, 44800 faces slice 100: 54830 vertices, 55159 faces slice 110: 63185 vertices, 63499 faces slice 120: 71429 vertices, 71762 faces slice 130: 78581 vertices, 78875 faces slice 140: 85683 vertices, 85958 faces slice 150: 91348 vertices, 91540 faces slice 160: 95826 vertices, 96008 faces slice 170: 99875 vertices, 100038 faces slice 180: 102929 vertices, 103063 faces slice 190: 105198 vertices, 105306 faces slice 200: 106651 vertices, 106715 faces slice 210: 107086 vertices, 107114 faces slice 220: 107086 vertices, 107114 faces slice 230: 107086 vertices, 107114 faces slice 240: 107086 vertices, 107114 faces slice 250: 107086 vertices, 107114 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 107086 voxel in cpt #1: X=-28 [v=107086,e=321342,f=214228] located at (32.848721, -26.857199, 8.483042) For the whole surface: X=-28 [v=107086,e=321342,f=214228] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Mon Nov 14 19:56:04 CET 2022 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Mon Nov 14 19:56:07 CET 2022 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 48.6 mm, total surface area = 62689 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.076 (target=0.015) step 005: RMS=0.059 (target=0.015) step 010: RMS=0.046 (target=0.015) step 015: RMS=0.042 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #------------------------------------------ Started at Mon Nov 14 19:55:05 CET 2022 Ended at Mon Nov 14 19:56:29 CET 2022 #@#%# recon-all-run-time-hours 0.023 recon-all -s Luce finished without error at Mon Nov 14 19:56:30 CET 2022 New invocation of recon-all Mon Nov 14 20:07:06 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce ./recon-allXL -s Luce -autorecon2-wm -noaseg -cc-crs 128 108 129 -pons-crs 128, 184, 82 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gbw-d-l0047 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257143 maxlocks unlimited maxsignal 257143 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880800 15598408 38802612 413416 11479780 49199752 Swap: 67108860 1036 67107824 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/11/14-19:07:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Mask BFS Mon Nov 14 20:07:11 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1658623 voxels in mask (pct= 9.89) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# Fill Mon Nov 14 20:07:12 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_fill -a ../scripts/ponscc.cut.log -Pv 128, 184, 82 -Cv 128 108 129 wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position (128, 184, 82) as pons seed point using voxel position (128, 108, 129) as corpus callosum seed point reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. Looking for area (min, max) = (350, 1400) area[0] = 2409 (min = 350, max = 1400), aspect = 0.71 (min = 0.10, max = 0.75) need search nearby using seed (128, 108, 129), TAL = (-34.7, -39.2, 89.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (-34.75, -39.20, 89.56) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (128, 184, 82), TAL = (-34.7, -86.2, 13.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (-34.75, -39.20, 89.56) Using voxel pons seed point, calculated talairach pons position (-34.75, -86.20, 13.56) find_cutting_plane:seed point not in structure! Searching neighborhood... done. filling left hemisphere... filling volume: pass 1 of 3...total of 219117 voxels filled... filling volume: pass 2 of 3...total of 16491322 voxels filled... filling volume: pass 3 of 3...total of 219337 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 216367 voxels filled... filling volume: pass 2 of 3...total of 16493889 voxels filled... filling volume: pass 3 of 3...total of 216770 voxels filled...done. filling degenerate left hemisphere surface locations... 778 voxels filled 3 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 900 voxels filled 7 voxels filled 0 voxels filled refilling left hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16490537 voxels filled... filling volume: pass 3 of 3...total of 220122 voxels filled...done. refilling right hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16492982 voxels filled... filling volume: pass 3 of 3...total of 217677 voxels filled...done. combining hemispheres... writing output to filled.mgz... filling took 0.2 minutes seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(-16.75, -39.20, 89.56) SRC: (110.00, 108.00, 129.00) search lh wm seed point around talairach space (-52.75, -39.20, 89.56), SRC: (146.00, 108.00, 129.00) #-------------------------------------------- #@# Tessellate lh Mon Nov 14 20:07:26 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 3 found - 3 modified | TOTAL: 5 pass 2 (xz+): 0 found - 3 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 2 found - 2 modified | TOTAL: 5 pass 2 (+++): 0 found - 2 modified | TOTAL: 5 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 4 found - 4 modified | TOTAL: 4 pass 2 (--): 1 found - 5 modified | TOTAL: 5 pass 3 (--): 0 found - 5 modified | TOTAL: 5 pass 1 (-+): 0 found - 0 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 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 : 4 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 : 4 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 = 22 (out of 220145: 0.009993) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 941 vertices, 1006 faces slice 40: 5230 vertices, 5370 faces slice 50: 11458 vertices, 11744 faces slice 60: 18263 vertices, 18490 faces slice 70: 25112 vertices, 25393 faces slice 80: 32719 vertices, 32977 faces slice 90: 42217 vertices, 42580 faces slice 100: 52594 vertices, 52924 faces slice 110: 61317 vertices, 61632 faces slice 120: 69539 vertices, 69874 faces slice 130: 77180 vertices, 77478 faces slice 140: 84238 vertices, 84529 faces slice 150: 90444 vertices, 90646 faces slice 160: 95245 vertices, 95428 faces slice 170: 99372 vertices, 99529 faces slice 180: 102491 vertices, 102626 faces slice 190: 104875 vertices, 104972 faces slice 200: 106140 vertices, 106204 faces slice 210: 106586 vertices, 106610 faces slice 220: 106586 vertices, 106610 faces slice 230: 106586 vertices, 106610 faces slice 240: 106586 vertices, 106610 faces slice 250: 106586 vertices, 106610 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 106586 voxel in cpt #1: X=-24 [v=106586,e=319830,f=213220] located at (-31.678738, -25.275534, 9.667865) For the whole surface: X=-24 [v=106586,e=319830,f=213220] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Nov 14 20:07:32 CET 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Nov 14 20:07:34 CET 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 48.0 mm, total surface area = 62194 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.076 (target=0.015) step 005: RMS=0.058 (target=0.015) step 010: RMS=0.045 (target=0.015) step 015: RMS=0.041 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Nov 14 20:07:56 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.14 +- 0.69 (0.00-->6.30) (max @ vno 86862 --> 86863) face area 0.03 +- 0.03 (-0.11-->0.46) scaling brain by 0.304... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=178.834, avgs=0 005/300: dt: 0.9000, rms radial error=178.579, avgs=0 010/300: dt: 0.9000, rms radial error=178.032, avgs=0 015/300: dt: 0.9000, rms radial error=177.312, avgs=0 020/300: dt: 0.9000, rms radial error=176.492, avgs=0 025/300: dt: 0.9000, rms radial error=175.612, avgs=0 030/300: dt: 0.9000, rms radial error=174.700, avgs=0 035/300: dt: 0.9000, rms radial error=173.769, avgs=0 040/300: dt: 0.9000, rms radial error=172.829, avgs=0 045/300: dt: 0.9000, rms radial error=171.886, avgs=0 050/300: dt: 0.9000, rms radial error=170.945, avgs=0 055/300: dt: 0.9000, rms radial error=170.008, avgs=0 060/300: dt: 0.9000, rms radial error=169.074, avgs=0 065/300: dt: 0.9000, rms radial error=168.143, avgs=0 070/300: dt: 0.9000, rms radial error=167.216, avgs=0 075/300: dt: 0.9000, rms radial error=166.294, avgs=0 080/300: dt: 0.9000, rms radial error=165.375, avgs=0 085/300: dt: 0.9000, rms radial error=164.460, avgs=0 090/300: dt: 0.9000, rms radial error=163.550, avgs=0 095/300: dt: 0.9000, rms radial error=162.645, avgs=0 100/300: dt: 0.9000, rms radial error=161.743, avgs=0 105/300: dt: 0.9000, rms radial error=160.846, avgs=0 110/300: dt: 0.9000, rms radial error=159.954, avgs=0 115/300: dt: 0.9000, rms radial error=159.066, avgs=0 120/300: dt: 0.9000, rms radial error=158.182, avgs=0 125/300: dt: 0.9000, rms radial error=157.303, avgs=0 130/300: dt: 0.9000, rms radial error=156.429, avgs=0 135/300: dt: 0.9000, rms radial error=155.558, avgs=0 140/300: dt: 0.9000, rms radial error=154.693, avgs=0 145/300: dt: 0.9000, rms radial error=153.831, avgs=0 150/300: dt: 0.9000, rms radial error=152.974, avgs=0 155/300: dt: 0.9000, rms radial error=152.122, avgs=0 160/300: dt: 0.9000, rms radial error=151.274, avgs=0 165/300: dt: 0.9000, rms radial error=150.431, avgs=0 170/300: dt: 0.9000, rms radial error=149.591, avgs=0 175/300: dt: 0.9000, rms radial error=148.757, avgs=0 180/300: dt: 0.9000, rms radial error=147.926, avgs=0 185/300: dt: 0.9000, rms radial error=147.101, avgs=0 190/300: dt: 0.9000, rms radial error=146.279, avgs=0 195/300: dt: 0.9000, rms radial error=145.462, avgs=0 200/300: dt: 0.9000, rms radial error=144.649, avgs=0 205/300: dt: 0.9000, rms radial error=143.840, avgs=0 210/300: dt: 0.9000, rms radial error=143.036, avgs=0 215/300: dt: 0.9000, rms radial error=142.236, avgs=0 220/300: dt: 0.9000, rms radial error=141.440, avgs=0 225/300: dt: 0.9000, rms radial error=140.648, avgs=0 230/300: dt: 0.9000, rms radial error=139.861, avgs=0 235/300: dt: 0.9000, rms radial error=139.078, avgs=0 240/300: dt: 0.9000, rms radial error=138.300, avgs=0 245/300: dt: 0.9000, rms radial error=137.525, avgs=0 250/300: dt: 0.9000, rms radial error=136.755, avgs=0 255/300: dt: 0.9000, rms radial error=135.989, avgs=0 260/300: dt: 0.9000, rms radial error=135.228, avgs=0 265/300: dt: 0.9000, rms radial error=134.470, avgs=0 270/300: dt: 0.9000, rms radial error=133.717, avgs=0 275/300: dt: 0.9000, rms radial error=132.967, avgs=0 280/300: dt: 0.9000, rms radial error=132.222, avgs=0 285/300: dt: 0.9000, rms radial error=131.481, avgs=0 290/300: dt: 0.9000, rms radial error=130.744, avgs=0 295/300: dt: 0.9000, rms radial error=130.011, avgs=0 300/300: dt: 0.9000, rms radial error=129.282, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12336.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00023 epoch 2 (K=40.0), pass 1, starting sse = 2016.94 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 = 231.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00657 epoch 4 (K=640.0), pass 1, starting sse = 22.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.21/17 = 0.01238 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Nov 14 20:11:01 CET 2022 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Luce 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-24 (nv=106586, nf=213220, ne=319830, g=13) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 5900 ambiguous faces found in tessellation segmenting defects... 17 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 1 -merging segment 14 into 13 15 defects to be corrected 0 vertices coincident reading input surface /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2578 (-4.6289) -vertex loglikelihood: -6.8000 (-3.4000) -normal dot loglikelihood: -3.5912 (-3.5912) -quad curv loglikelihood: -5.9179 (-2.9589) Total Loglikelihood : -25.5667 CORRECTING DEFECT 0 (vertices=169, convex hull=112) After retessellation of defect 0, euler #=-11 (103295,309180,205874) : difference with theory (-12) = -1 CORRECTING DEFECT 1 (vertices=1619, convex hull=434) After retessellation of defect 1, euler #=-9 (103839,311031,207183) : difference with theory (-11) = -2 CORRECTING DEFECT 2 (vertices=945, convex hull=344) After retessellation of defect 2, euler #=-11 (104064,311887,207812) : difference with theory (-10) = 1 CORRECTING DEFECT 3 (vertices=9, convex hull=19) After retessellation of defect 3, euler #=-10 (104065,311896,207821) : difference with theory (-9) = 1 CORRECTING DEFECT 4 (vertices=34, convex hull=47) After retessellation of defect 4, euler #=-9 (104080,311959,207870) : difference with theory (-8) = 1 CORRECTING DEFECT 5 (vertices=38, convex hull=71) After retessellation of defect 5, euler #=-8 (104089,312019,207922) : difference with theory (-7) = 1 CORRECTING DEFECT 6 (vertices=57, convex hull=63) After retessellation of defect 6, euler #=-7 (104107,312098,207984) : difference with theory (-6) = 1 CORRECTING DEFECT 7 (vertices=28, convex hull=51) After retessellation of defect 7, euler #=-6 (104121,312160,208033) : difference with theory (-5) = 1 CORRECTING DEFECT 8 (vertices=17, convex hull=17) After retessellation of defect 8, euler #=-5 (104124,312173,208044) : difference with theory (-4) = 1 CORRECTING DEFECT 9 (vertices=15, convex hull=22) After retessellation of defect 9, euler #=-4 (104127,312186,208055) : difference with theory (-3) = 1 CORRECTING DEFECT 10 (vertices=38, convex hull=94) After retessellation of defect 10, euler #=-3 (104140,312261,208118) : difference with theory (-2) = 1 CORRECTING DEFECT 11 (vertices=218, convex hull=151) After retessellation of defect 11, euler #=-2 (104202,312519,208315) : difference with theory (-1) = 1 CORRECTING DEFECT 12 (vertices=101, convex hull=147) After retessellation of defect 12, euler #=0 (104215,312625,208410) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=7, convex hull=26) After retessellation of defect 13, euler #=1 (104216,312635,208420) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=10, convex hull=23) After retessellation of defect 14, euler #=2 (104218,312648,208432) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.03-->14.21) (max @ vno 12528 --> 103517) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.03-->14.21) (max @ vno 12528 --> 103517) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 55 mutations (32.9%), 112 crossovers (67.1%), 122 vertices were eliminated building final representation... 2368 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=104218, nf=208432, ne=312648, g=0) writing corrected surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 9.4 minutes 0 defective edges removing intersecting faces 000: 441 intersecting 001: 94 intersecting 002: 53 intersecting 003: 36 intersecting 004: 31 intersecting expanding nbhd size to 2 005: 34 intersecting 006: 30 intersecting 007: 22 intersecting 008: 14 intersecting 009: 12 intersecting 010: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 104218 - 312648 + 208432 = 2 --> 0 holes F =2V-4: 208432 = 208436-4 (0) 2E=3F: 625296 = 625296 (0) total defect index = 0 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 216 intersecting 001: 50 intersecting 002: 46 intersecting 003: 44 intersecting 004: 34 intersecting expanding nbhd size to 2 005: 39 intersecting expanding nbhd size to 3 006: 43 intersecting 007: 37 intersecting 008: 19 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Nov 14 20:20:33 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_make_surfaces -noaseg -noaparc -mgz -T1 brain.finalsurfs Luce lh not using aseg volume 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/filled.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/brain.finalsurfs.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/wm.mgz... 14861 bright wm thresholded. 109 bright non-wm voxels segmented. reading original surface position from /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.orig... computing class statistics... border white: 191838 voxels (1.14%) border gray 215903 voxels (1.29%) WM (94.0): 94.2 +- 8.9 [70.0 --> 110.0] GM (83.0) : 82.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.7 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.85 +- 0.24 (0.03-->7.42) (max @ vno 12528 --> 103358) face area 0.30 +- 0.14 (0.00-->6.53) mean absolute distance = 0.87 +- 1.29 3368 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=75 mean inside = 93.6, mean outside = 77.5 smoothing surface for 5 iterations... mean border=83.9, 856 (856) missing vertices, mean dist 0.2 [1.1 (%33.3)->0.8 (%66.7))] %65 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, 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 0.90 +- 0.27 (0.06-->7.03) (max @ vno 20143 --> 103730) face area 0.30 +- 0.16 (0.00-->6.89) mean absolute distance = 0.49 +- 0.74 5101 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4144519.0, rms=11.70 001: dt: 0.5000, sse=4339127.5, rms=8.524 (0.000%) 002: dt: 0.5000, sse=4397770.0, rms=6.613 (0.000%) 003: dt: 0.5000, sse=4779519.5, rms=5.547 (0.000%) 004: dt: 0.5000, sse=4844988.0, rms=5.028 (0.000%) 005: dt: 0.5000, sse=5074069.0, rms=4.740 (0.000%) 006: dt: 0.5000, sse=5078731.0, rms=4.490 (0.000%) 007: dt: 0.5000, sse=5225535.5, rms=4.279 (0.000%) 008: dt: 0.5000, sse=5196314.5, rms=4.175 (0.000%) 009: dt: 0.5000, sse=5329134.5, rms=4.019 (0.000%) 010: dt: 0.5000, sse=5254802.5, rms=3.907 (0.000%) 011: dt: 0.5000, sse=5356139.5, rms=3.793 (0.000%) rms = 3.76, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=5282017.5, rms=3.758 (0.000%) 013: dt: 0.2500, sse=3245929.5, rms=3.030 (0.000%) 014: dt: 0.2500, sse=3087587.0, rms=2.859 (0.000%) 015: dt: 0.2500, sse=2951691.5, rms=2.803 (0.000%) rms = 2.76, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=2929956.2, rms=2.758 (0.000%) rms = 2.72, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=2869134.5, rms=2.717 (0.000%) positioning took 1.4 minutes mean border=87.7, 944 (375) missing vertices, mean dist -0.4 [0.6 (%77.5)->0.3 (%22.5))] %85 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, 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 +- 0.27 (0.01-->7.19) (max @ vno 20143 --> 103730) face area 0.34 +- 0.18 (0.00-->7.39) mean absolute distance = 0.24 +- 0.48 2881 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3511150.2, rms=5.95 018: dt: 0.5000, sse=3476769.2, rms=4.533 (0.000%) 019: dt: 0.5000, sse=3904779.2, rms=4.148 (0.000%) 020: dt: 0.5000, sse=4368170.5, rms=4.009 (0.000%) 021: dt: 0.5000, sse=4664683.5, rms=3.942 (0.000%) 022: dt: 0.5000, sse=4823939.5, rms=3.830 (0.000%) 023: dt: 0.5000, sse=4961212.5, rms=3.772 (0.000%) 024: dt: 0.5000, sse=5011325.0, rms=3.667 (0.000%) rms = 3.65, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=5062500.5, rms=3.650 (0.000%) 026: dt: 0.2500, sse=3152489.0, rms=2.665 (0.000%) 027: dt: 0.2500, sse=3046620.8, rms=2.450 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=2884601.2, rms=2.400 (0.000%) rms = 2.36, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=2831180.8, rms=2.355 (0.000%) positioning took 1.0 minutes mean border=88.5, 949 (262) missing vertices, mean dist -0.1 [0.3 (%59.3)->0.2 (%40.7))] %88 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, 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 0.90 +- 0.27 (0.06-->7.10) (max @ vno 20143 --> 103730) face area 0.34 +- 0.18 (0.00-->7.35) mean absolute distance = 0.23 +- 0.39 2868 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2879637.8, rms=2.83 rms = 2.82, time step reduction 1 of 3 to 0.250... 030: dt: 0.5000, sse=3086991.0, rms=2.825 (0.000%) 031: dt: 0.2500, sse=2982221.8, rms=2.474 (0.000%) 032: dt: 0.2500, sse=2951580.8, rms=2.385 (0.000%) rms = 2.38, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=2897874.8, rms=2.376 (0.000%) rms = 2.33, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=2854609.5, rms=2.330 (0.000%) positioning took 0.4 minutes mean border=88.8, 1080 (229) missing vertices, mean dist -0.0 [0.3 (%52.0)->0.2 (%48.0))] %89 local maxima, %10 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, 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 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=2872439.0, rms=2.51 035: dt: 0.5000, sse=3900376.5, rms=2.443 (0.000%) rms = 2.76, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3482238.2, rms=2.205 (0.000%) rms = 2.21, time step reduction 2 of 3 to 0.125... rms = 2.17, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=3436878.5, rms=2.170 (0.000%) positioning took 0.3 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.area vertex spacing 0.90 +- 0.27 (0.07-->7.13) (max @ vno 20143 --> 103730) face area 0.34 +- 0.19 (0.00-->6.90) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=59.2, 361 (361) missing vertices, mean dist 3.9 [1.8 (%0.2)->4.2 (%99.8))] %55 local maxima, %37 large gradients and % 8 min vals, 869 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_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 = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=20744120.0, rms=30.65 001: dt: 0.5000, sse=15798542.0, rms=26.400 (0.000%) 002: dt: 0.5000, sse=12389659.0, rms=22.960 (0.000%) 003: dt: 0.5000, sse=10291573.0, rms=20.488 (0.000%) 004: dt: 0.5000, sse=9214451.0, rms=18.926 (0.000%) 005: dt: 0.5000, sse=8647537.0, rms=17.982 (0.000%) 006: dt: 0.5000, sse=8332812.0, rms=17.340 (0.000%) 007: dt: 0.5000, sse=8014116.0, rms=16.698 (0.000%) 008: dt: 0.5000, sse=7727559.5, rms=15.999 (0.000%) 009: dt: 0.5000, sse=7393853.0, rms=15.201 (0.000%) 010: dt: 0.5000, sse=7133809.5, rms=14.360 (0.000%) 011: dt: 0.5000, sse=6881305.0, rms=13.440 (0.000%) 012: dt: 0.5000, sse=6643232.0, rms=12.492 (0.000%) 013: dt: 0.5000, sse=6403116.5, rms=11.521 (0.000%) 014: dt: 0.5000, sse=6299574.0, rms=10.702 (0.000%) 015: dt: 0.5000, sse=6275115.0, rms=10.004 (0.000%) 016: dt: 0.5000, sse=6279436.5, rms=9.391 (0.000%) 017: dt: 0.5000, sse=6252653.0, rms=8.776 (0.000%) 018: dt: 0.5000, sse=6247608.0, rms=8.222 (0.000%) 019: dt: 0.5000, sse=6212578.5, rms=7.668 (0.000%) 020: dt: 0.5000, sse=6205411.5, rms=7.223 (0.000%) 021: dt: 0.5000, sse=6165743.0, rms=6.808 (0.000%) 022: dt: 0.5000, sse=6213803.0, rms=6.488 (0.000%) 023: dt: 0.5000, sse=6184003.0, rms=6.177 (0.000%) 024: dt: 0.5000, sse=6199984.5, rms=5.975 (0.000%) 025: dt: 0.5000, sse=6199152.5, rms=5.758 (0.000%) 026: dt: 0.5000, sse=6178754.5, rms=5.634 (0.000%) 027: dt: 0.5000, sse=6176003.5, rms=5.495 (0.000%) 028: dt: 0.5000, sse=6180492.5, rms=5.441 (0.000%) 029: dt: 0.5000, sse=6159433.5, rms=5.359 (0.000%) rms = 5.37, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=4403471.0, rms=4.288 (0.000%) positioning took 2.0 minutes mean border=55.2, 621 (88) missing vertices, mean dist 0.3 [0.3 (%24.0)->0.5 (%76.0))] %68 local maxima, %25 large gradients and % 6 min vals, 459 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, nav=8, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5329016.0, rms=7.18 031: dt: 0.5000, sse=5470436.5, rms=6.047 (0.000%) 032: dt: 0.5000, sse=5962517.0, rms=5.799 (0.000%) rms = 5.96, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4410605.5, rms=4.588 (0.000%) 034: dt: 0.2500, sse=3913224.0, rms=4.330 (0.000%) rms = 4.36, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=3691050.8, rms=4.087 (0.000%) 036: dt: 0.1250, sse=3382884.2, rms=3.731 (0.000%) 037: dt: 0.1250, sse=3313916.2, rms=3.612 (0.000%) rms = 3.57, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3298061.0, rms=3.575 (0.000%) positioning took 0.6 minutes mean border=53.5, 834 (58) missing vertices, mean dist 0.1 [0.3 (%29.8)->0.3 (%70.2))] %75 local maxima, %18 large gradients and % 5 min vals, 382 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, nav=4, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3432531.0, rms=4.47 rms = 5.83, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3265922.8, rms=3.836 (0.000%) 040: dt: 0.2500, sse=3265706.8, rms=3.744 (0.000%) rms = 3.84, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=3209344.8, rms=3.639 (0.000%) 042: dt: 0.1250, sse=3167407.8, rms=3.494 (0.000%) 043: dt: 0.1250, sse=3166711.5, rms=3.423 (0.000%) rms = 3.39, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=3181769.8, rms=3.385 (0.000%) positioning took 0.5 minutes mean border=53.0, 1589 (45) missing vertices, mean dist 0.0 [0.2 (%41.0)->0.2 (%59.0))] %78 local maxima, %15 large gradients and % 5 min vals, 414 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, nav=2, nbrs=2, l_surf_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 pial surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3210704.8, rms=3.60 rms = 4.71, time step reduction 1 of 3 to 0.250... 045: dt: 0.2500, sse=3167849.5, rms=3.358 (0.000%) 046: dt: 0.2500, sse=3370704.2, rms=3.302 (0.000%) rms = 3.48, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=3324787.0, rms=3.229 (0.000%) 048: dt: 0.1250, sse=3298826.8, rms=3.156 (0.000%) 049: dt: 0.1250, sse=3305494.5, rms=3.100 (0.000%) rms = 3.07, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=3320172.0, rms=3.068 (0.000%) positioning took 0.5 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.area.pial vertex spacing 1.04 +- 0.48 (0.09-->6.11) (max @ vno 103870 --> 103941) face area 0.43 +- 0.35 (0.00-->7.54) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 104218 vertices processed 25000 of 104218 vertices processed 50000 of 104218 vertices processed 75000 of 104218 vertices processed 100000 of 104218 vertices processed 0 of 104218 vertices processed 25000 of 104218 vertices processed 50000 of 104218 vertices processed 75000 of 104218 vertices processed 100000 of 104218 vertices processed thickness calculation complete, 23594:30849 truncations. 24862 vertices at 0 distance 68179 vertices at 1 distance 59386 vertices at 2 distance 31338 vertices at 3 distance 14186 vertices at 4 distance 5984 vertices at 5 distance 2487 vertices at 6 distance 1055 vertices at 7 distance 451 vertices at 8 distance 184 vertices at 9 distance 81 vertices at 10 distance 59 vertices at 11 distance 37 vertices at 12 distance 28 vertices at 13 distance 22 vertices at 14 distance 25 vertices at 15 distance 15 vertices at 16 distance 28 vertices at 17 distance 19 vertices at 18 distance 4 vertices at 19 distance 6 vertices at 20 distance writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.thickness positioning took 9.1 minutes #-------------------------------------------- #@# Smooth2 lh Mon Nov 14 20:29:37 CET 2022 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts 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 Mon Nov 14 20:29:40 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.6 mm, total surface area = 65572 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.086 (target=0.015) step 005: RMS=0.064 (target=0.015) step 010: RMS=0.049 (target=0.015) step 015: RMS=0.041 (target=0.015) step 020: RMS=0.036 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.020 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.018 (target=0.015) step 060: RMS=0.017 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 178 vertices thresholded to be in k1 ~ [-0.67 0.49], k2 ~ [-0.15 0.06] total integrated curvature = 0.485*4pi (6.100) --> 1 handles ICI = 1.7, FI = 20.1, variation=299.369 86 vertices thresholded to be in [-0.01 0.05] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.003 105 vertices thresholded to be in [-0.33 0.24] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.022, std = 0.041 done. #----------------------------------------- #@# Curvature Stats lh Mon Nov 14 20:30:56 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Luce 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 [ Luce/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 [ 171 ] Gb_filter = 0 WARN: S lookup min: -0.492677 WARN: S explicit min: 0.000000 vertex = 11 #-------------------------------------------- #@# Tessellate rh Mon Nov 14 20:30:59 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 5 found - 5 modified | TOTAL: 7 pass 2 (xz-): 0 found - 5 modified | TOTAL: 7 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 : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 217688: 0.004594) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 1422 vertices, 1511 faces slice 40: 6072 vertices, 6220 faces slice 50: 13257 vertices, 13510 faces slice 60: 19545 vertices, 19774 faces slice 70: 26873 vertices, 27141 faces slice 80: 34482 vertices, 34779 faces slice 90: 44425 vertices, 44800 faces slice 100: 54830 vertices, 55159 faces slice 110: 63185 vertices, 63499 faces slice 120: 71429 vertices, 71762 faces slice 130: 78581 vertices, 78875 faces slice 140: 85683 vertices, 85958 faces slice 150: 91348 vertices, 91540 faces slice 160: 95826 vertices, 96008 faces slice 170: 99875 vertices, 100038 faces slice 180: 102929 vertices, 103063 faces slice 190: 105198 vertices, 105306 faces slice 200: 106651 vertices, 106715 faces slice 210: 107086 vertices, 107114 faces slice 220: 107086 vertices, 107114 faces slice 230: 107086 vertices, 107114 faces slice 240: 107086 vertices, 107114 faces slice 250: 107086 vertices, 107114 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 107086 voxel in cpt #1: X=-28 [v=107086,e=321342,f=214228] located at (32.848721, -26.857199, 8.483042) For the whole surface: X=-28 [v=107086,e=321342,f=214228] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Mon Nov 14 20:31:05 CET 2022 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Mon Nov 14 20:31:08 CET 2022 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts avg radius = 48.6 mm, total surface area = 62689 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.076 (target=0.015) step 005: RMS=0.059 (target=0.015) step 010: RMS=0.046 (target=0.015) step 015: RMS=0.042 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Mon Nov 14 20:31:30 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.13 +- 0.69 (0.00-->5.90) (max @ vno 52653 --> 52654) face area 0.03 +- 0.03 (-0.12-->0.43) scaling brain by 0.300... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=178.808, avgs=0 005/300: dt: 0.9000, rms radial error=178.553, avgs=0 010/300: dt: 0.9000, rms radial error=178.006, avgs=0 015/300: dt: 0.9000, rms radial error=177.286, avgs=0 020/300: dt: 0.9000, rms radial error=176.466, avgs=0 025/300: dt: 0.9000, rms radial error=175.586, avgs=0 030/300: dt: 0.9000, rms radial error=174.673, avgs=0 035/300: dt: 0.9000, rms radial error=173.748, avgs=0 040/300: dt: 0.9000, rms radial error=172.816, avgs=0 045/300: dt: 0.9000, rms radial error=171.881, avgs=0 050/300: dt: 0.9000, rms radial error=170.946, avgs=0 055/300: dt: 0.9000, rms radial error=170.012, avgs=0 060/300: dt: 0.9000, rms radial error=169.080, avgs=0 065/300: dt: 0.9000, rms radial error=168.152, avgs=0 070/300: dt: 0.9000, rms radial error=167.228, avgs=0 075/300: dt: 0.9000, rms radial error=166.307, avgs=0 080/300: dt: 0.9000, rms radial error=165.391, avgs=0 085/300: dt: 0.9000, rms radial error=164.478, avgs=0 090/300: dt: 0.9000, rms radial error=163.570, avgs=0 095/300: dt: 0.9000, rms radial error=162.666, avgs=0 100/300: dt: 0.9000, rms radial error=161.767, avgs=0 105/300: dt: 0.9000, rms radial error=160.871, avgs=0 110/300: dt: 0.9000, rms radial error=159.981, avgs=0 115/300: dt: 0.9000, rms radial error=159.094, avgs=0 120/300: dt: 0.9000, rms radial error=158.212, avgs=0 125/300: dt: 0.9000, rms radial error=157.334, avgs=0 130/300: dt: 0.9000, rms radial error=156.461, avgs=0 135/300: dt: 0.9000, rms radial error=155.593, avgs=0 140/300: dt: 0.9000, rms radial error=154.728, avgs=0 145/300: dt: 0.9000, rms radial error=153.868, avgs=0 150/300: dt: 0.9000, rms radial error=153.012, avgs=0 155/300: dt: 0.9000, rms radial error=152.161, avgs=0 160/300: dt: 0.9000, rms radial error=151.314, avgs=0 165/300: dt: 0.9000, rms radial error=150.471, avgs=0 170/300: dt: 0.9000, rms radial error=149.633, avgs=0 175/300: dt: 0.9000, rms radial error=148.799, avgs=0 180/300: dt: 0.9000, rms radial error=147.970, avgs=0 185/300: dt: 0.9000, rms radial error=147.145, avgs=0 190/300: dt: 0.9000, rms radial error=146.324, avgs=0 195/300: dt: 0.9000, rms radial error=145.508, avgs=0 200/300: dt: 0.9000, rms radial error=144.696, avgs=0 205/300: dt: 0.9000, rms radial error=143.889, avgs=0 210/300: dt: 0.9000, rms radial error=143.086, avgs=0 215/300: dt: 0.9000, rms radial error=142.286, avgs=0 220/300: dt: 0.9000, rms radial error=141.492, avgs=0 225/300: dt: 0.9000, rms radial error=140.701, avgs=0 230/300: dt: 0.9000, rms radial error=139.915, avgs=0 235/300: dt: 0.9000, rms radial error=139.132, avgs=0 240/300: dt: 0.9000, rms radial error=138.354, avgs=0 245/300: dt: 0.9000, rms radial error=137.581, avgs=0 250/300: dt: 0.9000, rms radial error=136.811, avgs=0 255/300: dt: 0.9000, rms radial error=136.046, avgs=0 260/300: dt: 0.9000, rms radial error=135.285, avgs=0 265/300: dt: 0.9000, rms radial error=134.528, avgs=0 270/300: dt: 0.9000, rms radial error=133.775, avgs=0 275/300: dt: 0.9000, rms radial error=133.026, avgs=0 280/300: dt: 0.9000, rms radial error=132.282, avgs=0 285/300: dt: 0.9000, rms radial error=131.541, avgs=0 290/300: dt: 0.9000, rms radial error=130.805, avgs=0 295/300: dt: 0.9000, rms radial error=130.072, avgs=0 300/300: dt: 0.9000, rms radial error=129.344, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12437.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00026 epoch 2 (K=40.0), pass 1, starting sse = 2052.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 241.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00599 epoch 4 (K=640.0), pass 1, starting sse = 22.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/18 = 0.01079 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Mon Nov 14 20:34:38 CET 2022 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Luce rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-28 (nv=107086, nf=214228, ne=321342, g=15) 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... 5026 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 6 -merging segment 19 into 20 20 defects to be corrected 0 vertices coincident reading input surface /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2577 (-4.6289) -vertex loglikelihood: -6.8304 (-3.4152) -normal dot loglikelihood: -3.5523 (-3.5523) -quad curv loglikelihood: -5.5954 (-2.7977) Total Loglikelihood : -25.2359 CORRECTING DEFECT 0 (vertices=1073, convex hull=269) After retessellation of defect 0, euler #=-18 (104457,312616,208141) : difference with theory (-17) = 1 CORRECTING DEFECT 1 (vertices=20, convex hull=45) After retessellation of defect 1, euler #=-17 (104465,312654,208172) : difference with theory (-16) = 1 CORRECTING DEFECT 2 (vertices=450, convex hull=193) After retessellation of defect 2, euler #=-16 (104556,313022,208450) : difference with theory (-15) = 1 CORRECTING DEFECT 3 (vertices=9, convex hull=23) After retessellation of defect 3, euler #=-15 (104557,313030,208458) : difference with theory (-14) = 1 CORRECTING DEFECT 4 (vertices=195, convex hull=189) After retessellation of defect 4, euler #=-14 (104634,313346,208698) : difference with theory (-13) = 1 CORRECTING DEFECT 5 (vertices=250, convex hull=213) After retessellation of defect 5, euler #=-13 (104778,313879,209088) : difference with theory (-12) = 1 CORRECTING DEFECT 6 (vertices=480, convex hull=293) After retessellation of defect 6, euler #=-11 (104922,314473,209540) : difference with theory (-11) = 0 CORRECTING DEFECT 7 (vertices=15, convex hull=21) After retessellation of defect 7, euler #=-10 (104925,314489,209554) : difference with theory (-10) = 0 CORRECTING DEFECT 8 (vertices=11, convex hull=27) After retessellation of defect 8, euler #=-9 (104926,314501,209566) : difference with theory (-9) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=30) After retessellation of defect 9, euler #=-8 (104930,314520,209582) : difference with theory (-8) = 0 CORRECTING DEFECT 10 (vertices=28, convex hull=52) After retessellation of defect 10, euler #=-7 (104942,314575,209626) : difference with theory (-7) = 0 CORRECTING DEFECT 11 (vertices=6, convex hull=26) After retessellation of defect 11, euler #=-6 (104945,314591,209640) : difference with theory (-6) = 0 CORRECTING DEFECT 12 (vertices=94, convex hull=95) After retessellation of defect 12, euler #=-6 (104982,314750,209762) : difference with theory (-5) = 1 CORRECTING DEFECT 13 (vertices=60, convex hull=100) After retessellation of defect 13, euler #=-5 (105013,314883,209865) : difference with theory (-4) = 1 CORRECTING DEFECT 14 (vertices=15, convex hull=34) After retessellation of defect 14, euler #=-4 (105017,314907,209886) : difference with theory (-3) = 1 CORRECTING DEFECT 15 (vertices=8, convex hull=25) After retessellation of defect 15, euler #=-3 (105019,314921,209899) : difference with theory (-2) = 1 CORRECTING DEFECT 16 (vertices=14, convex hull=17) After retessellation of defect 16, euler #=-2 (105021,314934,209911) : difference with theory (-1) = 1 CORRECTING DEFECT 17 (vertices=23, convex hull=59) After retessellation of defect 17, euler #=-1 (105034,314995,209960) : difference with theory (0) = 1 CORRECTING DEFECT 18 (vertices=157, convex hull=157) After retessellation of defect 18, euler #=1 (105075,315200,210126) : difference with theory (1) = 0 CORRECTING DEFECT 19 (vertices=22, convex hull=46) After retessellation of defect 19, euler #=2 (105079,315231,210154) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.25 (0.07-->8.61) (max @ vno 21228 --> 104766) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.25 (0.07-->8.61) (max @ vno 21228 --> 104766) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 90 mutations (38.6%), 143 crossovers (61.4%), 153 vertices were eliminated building final representation... 2007 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=105079, nf=210154, ne=315231, g=0) writing corrected surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 22.9 minutes 0 defective edges removing intersecting faces 000: 353 intersecting 001: 27 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 105079 - 315231 + 210154 = 2 --> 0 holes F =2V-4: 210154 = 210158-4 (0) 2E=3F: 630462 = 630462 (0) total defect index = 0 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 91 intersecting 001: 8 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Mon Nov 14 20:57:34 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_make_surfaces -noaseg -noaparc -mgz -T1 brain.finalsurfs Luce rh not using aseg volume 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/filled.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/brain.finalsurfs.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/wm.mgz... 13039 bright wm thresholded. 111 bright non-wm voxels segmented. reading original surface position from /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.orig... computing class statistics... border white: 191838 voxels (1.14%) border gray 215903 voxels (1.29%) WM (94.0): 94.2 +- 8.8 [70.0 --> 110.0] GM (83.0) : 82.3 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.1 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 54.2 (was 40) setting MAX_GRAY to 92.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.85 +- 0.24 (0.03-->7.58) (max @ vno 104313 --> 104434) face area 0.30 +- 0.16 (0.00-->14.13) mean absolute distance = 0.86 +- 1.27 3290 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=76 mean inside = 94.1, mean outside = 78.7 smoothing surface for 5 iterations... mean border=84.6, 1027 (1027) missing vertices, mean dist 0.2 [1.0 (%31.7)->0.8 (%68.3))] %62 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.27 (0.08-->8.09) (max @ vno 104313 --> 104434) face area 0.30 +- 0.17 (0.00-->12.37) mean absolute distance = 0.51 +- 0.76 5773 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3763947.8, rms=10.92 001: dt: 0.5000, sse=4005503.5, rms=7.668 (0.000%) 002: dt: 0.5000, sse=4176420.5, rms=5.802 (0.000%) 003: dt: 0.5000, sse=4582137.5, rms=4.872 (0.000%) 004: dt: 0.5000, sse=4722602.5, rms=4.484 (0.000%) 005: dt: 0.5000, sse=4972747.0, rms=4.283 (0.000%) 006: dt: 0.5000, sse=5024363.5, rms=4.117 (0.000%) 007: dt: 0.5000, sse=5227370.0, rms=3.982 (0.000%) 008: dt: 0.5000, sse=5189537.0, rms=3.852 (0.000%) 009: dt: 0.5000, sse=5329058.0, rms=3.729 (0.000%) 010: dt: 0.5000, sse=5290582.5, rms=3.633 (0.000%) 011: dt: 0.5000, sse=5392523.0, rms=3.546 (0.000%) 012: dt: 0.5000, sse=5333828.0, rms=3.492 (0.000%) 013: dt: 0.5000, sse=5402099.0, rms=3.436 (0.000%) rms = 3.41, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=5348729.0, rms=3.413 (0.000%) 015: dt: 0.2500, sse=3290070.0, rms=2.702 (0.000%) 016: dt: 0.2500, sse=3147118.8, rms=2.538 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3022060.2, rms=2.503 (0.000%) rms = 2.46, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=2959169.2, rms=2.464 (0.000%) positioning took 1.3 minutes mean border=88.1, 1012 (501) missing vertices, mean dist -0.4 [0.6 (%76.0)->0.3 (%24.0))] %82 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, 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 +- 0.27 (0.07-->8.38) (max @ vno 104313 --> 104434) face area 0.34 +- 0.20 (0.00-->14.74) mean absolute distance = 0.26 +- 0.49 3309 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3553682.2, rms=5.61 019: dt: 0.5000, sse=3518743.5, rms=4.277 (0.000%) 020: dt: 0.5000, sse=4013066.0, rms=3.890 (0.000%) 021: dt: 0.5000, sse=4404510.0, rms=3.753 (0.000%) rms = 3.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=4815391.5, rms=3.711 (0.000%) 023: dt: 0.2500, sse=3336980.5, rms=2.972 (0.000%) 024: dt: 0.2500, sse=3239584.8, rms=2.745 (0.000%) 025: dt: 0.2500, sse=3101960.5, rms=2.620 (0.000%) 026: dt: 0.2500, sse=3065884.5, rms=2.513 (0.000%) 027: dt: 0.2500, sse=3034770.2, rms=2.456 (0.000%) rms = 2.42, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=3022147.0, rms=2.418 (0.000%) rms = 2.39, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=2970163.5, rms=2.389 (0.000%) positioning took 0.8 minutes mean border=88.9, 1022 (389) missing vertices, mean dist -0.1 [0.3 (%58.4)->0.2 (%41.6))] %85 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, 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 0.90 +- 0.27 (0.04-->8.45) (max @ vno 104313 --> 104434) face area 0.34 +- 0.21 (0.00-->14.76) mean absolute distance = 0.25 +- 0.41 2745 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3021173.8, rms=2.87 030: dt: 0.5000, sse=3272305.2, rms=2.816 (0.000%) rms = 2.89, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3089405.2, rms=2.553 (0.000%) 032: dt: 0.2500, sse=3121274.5, rms=2.443 (0.000%) rms = 2.42, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3065451.8, rms=2.416 (0.000%) rms = 2.38, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=3022292.8, rms=2.375 (0.000%) positioning took 0.4 minutes mean border=89.2, 1181 (361) missing vertices, mean dist -0.1 [0.3 (%51.8)->0.2 (%48.2))] %87 local maxima, %12 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, 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 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3035376.5, rms=2.51 035: dt: 0.5000, sse=4139221.5, rms=2.399 (0.000%) rms = 2.64, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3687506.0, rms=2.183 (0.000%) rms = 2.18, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=3481268.5, rms=2.180 (0.000%) 038: dt: 0.1250, sse=3469871.5, rms=2.091 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=3466765.5, rms=2.060 (0.000%) positioning took 0.4 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.area vertex spacing 0.90 +- 0.27 (0.04-->8.64) (max @ vno 104313 --> 104434) face area 0.34 +- 0.21 (0.00-->14.80) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.2, 444 (444) missing vertices, mean dist 3.9 [1.5 (%0.2)->4.2 (%99.8))] %57 local maxima, %35 large gradients and % 7 min vals, 635 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_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 = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=20014462.0, rms=29.94 001: dt: 0.5000, sse=15470896.0, rms=25.997 (0.000%) 002: dt: 0.5000, sse=12288269.0, rms=22.764 (0.000%) 003: dt: 0.5000, sse=10331095.0, rms=20.420 (0.000%) 004: dt: 0.5000, sse=9208333.0, rms=18.821 (0.000%) 005: dt: 0.5000, sse=8631784.0, rms=17.808 (0.000%) 006: dt: 0.5000, sse=8241504.5, rms=17.051 (0.000%) 007: dt: 0.5000, sse=7955402.5, rms=16.365 (0.000%) 008: dt: 0.5000, sse=7617363.5, rms=15.623 (0.000%) 009: dt: 0.5000, sse=7372869.0, rms=14.866 (0.000%) 010: dt: 0.5000, sse=7055927.0, rms=14.055 (0.000%) 011: dt: 0.5000, sse=6850848.5, rms=13.220 (0.000%) 012: dt: 0.5000, sse=6554420.5, rms=12.304 (0.000%) 013: dt: 0.5000, sse=6394215.5, rms=11.452 (0.000%) 014: dt: 0.5000, sse=6227741.0, rms=10.667 (0.000%) 015: dt: 0.5000, sse=6254127.0, rms=10.021 (0.000%) 016: dt: 0.5000, sse=6152034.5, rms=9.376 (0.000%) 017: dt: 0.5000, sse=6190779.5, rms=8.780 (0.000%) 018: dt: 0.5000, sse=6106203.5, rms=8.182 (0.000%) 019: dt: 0.5000, sse=6117042.0, rms=7.669 (0.000%) 020: dt: 0.5000, sse=6096858.5, rms=7.188 (0.000%) 021: dt: 0.5000, sse=6109951.5, rms=6.812 (0.000%) 022: dt: 0.5000, sse=6060525.5, rms=6.425 (0.000%) 023: dt: 0.5000, sse=6105616.0, rms=6.152 (0.000%) 024: dt: 0.5000, sse=6073152.0, rms=5.863 (0.000%) 025: dt: 0.5000, sse=6126736.5, rms=5.686 (0.000%) 026: dt: 0.5000, sse=6094058.5, rms=5.514 (0.000%) rms = 5.46, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=6128609.5, rms=5.465 (0.000%) 028: dt: 0.2500, sse=3904437.2, rms=4.346 (0.000%) 029: dt: 0.2500, sse=3791567.0, rms=4.060 (0.000%) rms = 4.07, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=3601908.0, rms=3.864 (0.000%) positioning took 2.1 minutes mean border=56.2, 603 (93) missing vertices, mean dist 0.3 [0.3 (%23.2)->0.5 (%76.8))] %71 local maxima, %23 large gradients and % 5 min vals, 399 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, nav=8, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4489521.0, rms=6.79 031: dt: 0.5000, sse=4917874.0, rms=6.096 (0.000%) 032: dt: 0.5000, sse=5355573.0, rms=5.670 (0.000%) rms = 6.00, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4127823.2, rms=4.516 (0.000%) 034: dt: 0.2500, sse=3789767.2, rms=4.230 (0.000%) rms = 4.30, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=3602699.5, rms=4.016 (0.000%) 036: dt: 0.1250, sse=3351390.2, rms=3.711 (0.000%) 037: dt: 0.1250, sse=3296800.0, rms=3.602 (0.000%) rms = 3.56, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3271046.8, rms=3.558 (0.000%) positioning took 0.6 minutes mean border=54.5, 812 (61) missing vertices, mean dist 0.1 [0.3 (%29.2)->0.3 (%70.8))] %78 local maxima, %16 large gradients and % 5 min vals, 389 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, nav=4, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3412814.2, rms=4.45 rms = 5.77, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3246327.0, rms=3.825 (0.000%) 040: dt: 0.2500, sse=3244489.5, rms=3.712 (0.000%) rms = 3.81, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=3188131.8, rms=3.609 (0.000%) 042: dt: 0.1250, sse=3148567.5, rms=3.468 (0.000%) 043: dt: 0.1250, sse=3145794.2, rms=3.392 (0.000%) 044: dt: 0.1250, sse=3158481.8, rms=3.340 (0.000%) rms = 3.31, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=3167510.0, rms=3.310 (0.000%) positioning took 0.6 minutes mean border=54.1, 1475 (54) missing vertices, mean dist 0.0 [0.2 (%40.6)->0.2 (%59.4))] %80 local maxima, %13 large gradients and % 5 min vals, 388 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, nav=2, nbrs=2, l_surf_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 pial surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3193565.0, rms=3.50 rms = 4.51, time step reduction 1 of 3 to 0.250... 046: dt: 0.2500, sse=3154093.2, rms=3.282 (0.000%) 047: dt: 0.2500, sse=3324799.0, rms=3.232 (0.000%) rms = 3.40, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=3279035.8, rms=3.159 (0.000%) 049: dt: 0.1250, sse=3248589.8, rms=3.081 (0.000%) rms = 3.04, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=3256239.5, rms=3.043 (0.000%) positioning took 0.4 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.area.pial vertex spacing 1.04 +- 0.48 (0.10-->6.40) (max @ vno 104313 --> 104434) face area 0.43 +- 0.35 (0.00-->7.12) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 105079 vertices processed 25000 of 105079 vertices processed 50000 of 105079 vertices processed 75000 of 105079 vertices processed 100000 of 105079 vertices processed 0 of 105079 vertices processed 25000 of 105079 vertices processed 50000 of 105079 vertices processed 75000 of 105079 vertices processed 100000 of 105079 vertices processed thickness calculation complete, 24081:31201 truncations. 25308 vertices at 0 distance 68410 vertices at 1 distance 60451 vertices at 2 distance 31719 vertices at 3 distance 14212 vertices at 4 distance 5868 vertices at 5 distance 2422 vertices at 6 distance 1003 vertices at 7 distance 376 vertices at 8 distance 129 vertices at 9 distance 57 vertices at 10 distance 39 vertices at 11 distance 22 vertices at 12 distance 29 vertices at 13 distance 35 vertices at 14 distance 18 vertices at 15 distance 20 vertices at 16 distance 13 vertices at 17 distance 5 vertices at 18 distance 6 vertices at 19 distance 16 vertices at 20 distance writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.thickness positioning took 8.7 minutes #-------------------------------------------- #@# Smooth2 rh Mon Nov 14 21:06:18 CET 2022 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Mon Nov 14 21:06:21 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 48.0 mm, total surface area = 66491 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.086 (target=0.015) step 005: RMS=0.064 (target=0.015) step 010: RMS=0.050 (target=0.015) step 015: RMS=0.041 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.020 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 103 vertices thresholded to be in k1 ~ [-0.61 0.38], k2 ~ [-0.16 0.18] total integrated curvature = 0.491*4pi (6.174) --> 1 handles ICI = 1.7, FI = 20.0, variation=300.346 72 vertices thresholded to be in [-0.02 0.05] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.003 88 vertices thresholded to be in [-0.29 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.022, std = 0.040 done. #----------------------------------------- #@# Curvature Stats rh Mon Nov 14 21:07:44 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Luce rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Luce/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 175 ] Gb_filter = 0 #------------------------------------------ Started at Mon Nov 14 20:07:06 CET 2022 Ended at Mon Nov 14 21:07:47 CET 2022 #@#%# recon-all-run-time-hours 1.011 recon-all -s Luce finished without error at Mon Nov 14 21:07:47 CET 2022 New invocation of recon-all Wed Nov 30 21:59:20 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce ./recon-allXL -s Luce -autorecon2-wmq -noaseg -cc-crs 128 108 129 -pons-crs 128 184 82 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-6.0.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux gbw-d-l0047 5.4.0-132-generic #148~18.04.1-Ubuntu SMP Mon Oct 24 20:41:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257143 maxlocks unlimited maxsignal 257143 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880824 1905188 60401048 73732 3574588 63232684 Swap: 67108860 0 67108860 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks 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: 2022/11/30-20:59:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-20:59:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-20:59:22-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:22-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:22-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:22-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:23-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:23-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:23-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-20:59:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-20:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-20:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-20:59:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-6.0.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-6.0.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /fmri/apps/freesurfer-6.0.0 Previous: /fmri/apps/freesurfer-5.3.0 #-------------------------------------------- #@# Fill Wed Nov 30 21:59:32 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_fill -a ../scripts/ponscc.cut.log -Pv 128 184 82 -Cv 128 108 129 wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position (128, 184, 82) as pons seed point using voxel position (128, 108, 129) as corpus callosum seed point reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using seed (128, 108, 129), TAL = (-34.7, -39.2, 89.6) talairach voxel to voxel transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Calculated talairach cc position (-34.75, -39.20, 89.56) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (128, 184, 82), TAL = (-34.7, -86.2, 13.6) talairach voxel to voxel transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; talairach cc position changed to (-34.75, -39.20, 89.56) Using voxel pons seed point, calculated talairach pons position (-34.75, -86.20, 13.56) find_cutting_plane:seed point not in structure! Searching neighborhood... done. filling left hemisphere... filling volume: pass 1 of 3...total of 213626 voxels filled... filling volume: pass 2 of 3...total of 16497023 voxels filled... filling volume: pass 3 of 3...total of 213636 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 214595 voxels filled... filling volume: pass 2 of 3...total of 16496039 voxels filled... filling volume: pass 3 of 3...total of 214620 voxels filled...done. filling degenerate left hemisphere surface locations... 671 voxels filled 1 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 708 voxels filled 0 voxels filled refilling left hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16496351 voxels filled... filling volume: pass 3 of 3...total of 214308 voxels filled...done. refilling right hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16495331 voxels filled... filling volume: pass 3 of 3...total of 215328 voxels filled...done. combining hemispheres... writing output to filled.mgz... filling took 0.2 minutes seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(-16.75, -39.20, 89.56) SRC: (110.00, 108.00, 129.00) search lh wm seed point around talairach space (-52.75, -39.20, 89.56), SRC: (146.00, 108.00, 129.00) #-------------------------------------------- #@# Tessellate lh Wed Nov 30 21:59:44 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1 (out of 214310: 0.000467) 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 30: 883 vertices, 949 faces slice 40: 5048 vertices, 5183 faces slice 50: 10976 vertices, 11238 faces slice 60: 17509 vertices, 17724 faces slice 70: 24193 vertices, 24457 faces slice 80: 31661 vertices, 31911 faces slice 90: 40280 vertices, 40605 faces slice 100: 49519 vertices, 49820 faces slice 110: 57601 vertices, 57892 faces slice 120: 65412 vertices, 65722 faces slice 130: 72354 vertices, 72612 faces slice 140: 78504 vertices, 78728 faces slice 150: 83951 vertices, 84124 faces slice 160: 88434 vertices, 88582 faces slice 170: 92330 vertices, 92457 faces slice 180: 95247 vertices, 95354 faces slice 190: 97385 vertices, 97453 faces slice 200: 98519 vertices, 98556 faces slice 210: 98856 vertices, 98858 faces slice 220: 98856 vertices, 98858 faces slice 230: 98856 vertices, 98858 faces slice 240: 98856 vertices, 98858 faces slice 250: 98856 vertices, 98858 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... 98856 voxel in cpt #1: X=-2 [v=98856,e=296574,f=197716] located at (-31.829084, -26.166393, 9.898195) For the whole surface: X=-2 [v=98856,e=296574,f=197716] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Nov 30 21:59:49 CET 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Nov 30 21:59:53 CET 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.0 mm, total surface area = 59065 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.106 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.067 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 23.587223 mris_inflate stimesec 0.083982 mris_inflate ru_maxrss 132720 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31466 mris_inflate ru_majflt 5 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1048 mris_inflate ru_oublock 6960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 138 mris_inflate ru_nivcsw 79 #-------------------------------------------- #@# Tessellate rh Wed Nov 30 22:00:17 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 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 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2 (out of 215331: 0.000929) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 1388 vertices, 1478 faces slice 40: 5898 vertices, 6040 faces slice 50: 12848 vertices, 13086 faces slice 60: 18821 vertices, 19040 faces slice 70: 25928 vertices, 26186 faces slice 80: 33301 vertices, 33583 faces slice 90: 42022 vertices, 42334 faces slice 100: 51190 vertices, 51490 faces slice 110: 59180 vertices, 59470 faces slice 120: 66996 vertices, 67298 faces slice 130: 73568 vertices, 73822 faces slice 140: 79905 vertices, 80139 faces slice 150: 84960 vertices, 85118 faces slice 160: 89144 vertices, 89287 faces slice 170: 93023 vertices, 93151 faces slice 180: 95833 vertices, 95934 faces slice 190: 97965 vertices, 98041 faces slice 200: 99303 vertices, 99338 faces slice 210: 99614 vertices, 99616 faces slice 220: 99614 vertices, 99616 faces slice 230: 99614 vertices, 99616 faces slice 240: 99614 vertices, 99616 faces slice 250: 99614 vertices, 99616 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 99614 voxel in cpt #1: X=-2 [v=99614,e=298848,f=199232] located at (32.838367, -27.505049, 8.674955) For the whole surface: X=-2 [v=99614,e=298848,f=199232] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Nov 30 22:00:22 CET 2022 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Nov 30 22:00:25 CET 2022 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 59546 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.107 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.067 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.052 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.028 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 24.764972 mris_inflate stimesec 0.135983 mris_inflate ru_maxrss 133780 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 45562 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7008 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 96 mris_inflate ru_nivcsw 63 #------------------------------------------ Started at Wed Nov 30 21:59:20 CET 2022 Ended at Wed Nov 30 22:00:50 CET 2022 #@#%# recon-all-run-time-hours 0.025 recon-all -s Luce finished without error at Wed Nov 30 22:00:50 CET 2022 New invocation of recon-all Wed Nov 30 22:11:37 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce ./recon-allXL -s Luce -autorecon2-wm -noaseg -cc-crs 128 108 129 -pons-crs 128 184 82 subjid Luce setenv SUBJECTS_DIR /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects FREESURFER_HOME /fmri/apps/freesurfer-6.0.0 Actual FREESURFER_HOME /mnt/.autofs/fmri/fmri/apps/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux gbw-d-l0047 5.4.0-132-generic #148~18.04.1-Ubuntu SMP Mon Oct 24 20:41:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 65536 kbytes maxproc 257143 maxlocks unlimited maxsignal 257143 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65880824 2309624 59555448 163524 4015752 62738452 Swap: 67108860 0 67108860 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks 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: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic 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: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2022/11/30-21:11:37-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: u0146233 Machine: gbw-d-l0047 Platform: Linux PlatformVersion: 5.4.0-132-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fmri/apps/freesurfer-6.0.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fmri/apps/freesurfer-6.0.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /fmri/apps/freesurfer-6.0.0 Previous: /fmri/apps/freesurfer-5.3.0 #-------------------------------------------- #@# Mask BFS Wed Nov 30 22:11:39 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1658623 voxels in mask (pct= 9.89) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# Fill Wed Nov 30 22:11:41 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri mri_fill -a ../scripts/ponscc.cut.log -Pv 128 184 82 -Cv 128 108 129 wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position (128, 184, 82) as pons seed point using voxel position (128, 108, 129) as corpus callosum seed point reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using seed (128, 108, 129), TAL = (-34.7, -39.2, 89.6) talairach voxel to voxel transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Calculated talairach cc position (-34.75, -39.20, 89.56) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (128, 184, 82), TAL = (-34.7, -86.2, 13.6) talairach voxel to voxel transform 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; talairach cc position changed to (-34.75, -39.20, 89.56) Using voxel pons seed point, calculated talairach pons position (-34.75, -86.20, 13.56) find_cutting_plane:seed point not in structure! Searching neighborhood... done. filling left hemisphere... filling volume: pass 1 of 3...total of 213626 voxels filled... filling volume: pass 2 of 3...total of 16497023 voxels filled... filling volume: pass 3 of 3...total of 213636 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 214595 voxels filled... filling volume: pass 2 of 3...total of 16496039 voxels filled... filling volume: pass 3 of 3...total of 214620 voxels filled...done. filling degenerate left hemisphere surface locations... 671 voxels filled 1 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 708 voxels filled 0 voxels filled refilling left hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16496351 voxels filled... filling volume: pass 3 of 3...total of 214308 voxels filled...done. refilling right hemisphere... filling volume: pass 1 of 3...total of 0 voxels filled... filling volume: pass 2 of 3...total of 16495331 voxels filled... filling volume: pass 3 of 3...total of 215328 voxels filled...done. combining hemispheres... writing output to filled.mgz... filling took 0.2 minutes seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(-16.75, -39.20, 89.56) SRC: (110.00, 108.00, 129.00) search lh wm seed point around talairach space (-52.75, -39.20, 89.56), SRC: (146.00, 108.00, 129.00) #-------------------------------------------- #@# Tessellate lh Wed Nov 30 22:11:53 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 255 ../mri/brain.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1 (out of 214310: 0.000467) 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 30: 883 vertices, 949 faces slice 40: 5048 vertices, 5183 faces slice 50: 10976 vertices, 11238 faces slice 60: 17509 vertices, 17724 faces slice 70: 24193 vertices, 24457 faces slice 80: 31661 vertices, 31911 faces slice 90: 40280 vertices, 40605 faces slice 100: 49519 vertices, 49820 faces slice 110: 57601 vertices, 57892 faces slice 120: 65412 vertices, 65722 faces slice 130: 72354 vertices, 72612 faces slice 140: 78504 vertices, 78728 faces slice 150: 83951 vertices, 84124 faces slice 160: 88434 vertices, 88582 faces slice 170: 92330 vertices, 92457 faces slice 180: 95247 vertices, 95354 faces slice 190: 97385 vertices, 97453 faces slice 200: 98519 vertices, 98556 faces slice 210: 98856 vertices, 98858 faces slice 220: 98856 vertices, 98858 faces slice 230: 98856 vertices, 98858 faces slice 240: 98856 vertices, 98858 faces slice 250: 98856 vertices, 98858 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... 98856 voxel in cpt #1: X=-2 [v=98856,e=296574,f=197716] located at (-31.829084, -26.166393, 9.898195) For the whole surface: X=-2 [v=98856,e=296574,f=197716] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Nov 30 22:11:57 CET 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Nov 30 22:12:01 CET 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.0 mm, total surface area = 59065 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.106 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.067 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 23.827650 mris_inflate stimesec 0.055999 mris_inflate ru_maxrss 132672 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31467 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 6960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 120 mris_inflate ru_nivcsw 79 #-------------------------------------------- #@# QSphere lh Wed Nov 30 22:12:25 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/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 1.17 +- 0.69 (0.00-->6.03) (max @ vno 56271 --> 57068) face area 0.03 +- 0.03 (-0.12-->0.40) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.309... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=178.581, avgs=0 005/300: dt: 0.9000, rms radial error=178.326, avgs=0 010/300: dt: 0.9000, rms radial error=177.778, avgs=0 015/300: dt: 0.9000, rms radial error=177.057, avgs=0 020/300: dt: 0.9000, rms radial error=176.238, avgs=0 025/300: dt: 0.9000, rms radial error=175.359, avgs=0 030/300: dt: 0.9000, rms radial error=174.447, avgs=0 035/300: dt: 0.9000, rms radial error=173.518, avgs=0 040/300: dt: 0.9000, rms radial error=172.579, avgs=0 045/300: dt: 0.9000, rms radial error=171.636, avgs=0 050/300: dt: 0.9000, rms radial error=170.692, avgs=0 055/300: dt: 0.9000, rms radial error=169.756, avgs=0 060/300: dt: 0.9000, rms radial error=168.823, avgs=0 065/300: dt: 0.9000, rms radial error=167.893, avgs=0 070/300: dt: 0.9000, rms radial error=166.966, avgs=0 075/300: dt: 0.9000, rms radial error=166.043, avgs=0 080/300: dt: 0.9000, rms radial error=165.125, avgs=0 085/300: dt: 0.9000, rms radial error=164.210, avgs=0 090/300: dt: 0.9000, rms radial error=163.300, avgs=0 095/300: dt: 0.9000, rms radial error=162.395, avgs=0 100/300: dt: 0.9000, rms radial error=161.494, avgs=0 105/300: dt: 0.9000, rms radial error=160.597, avgs=0 110/300: dt: 0.9000, rms radial error=159.705, avgs=0 115/300: dt: 0.9000, rms radial error=158.817, avgs=0 120/300: dt: 0.9000, rms radial error=157.934, avgs=0 125/300: dt: 0.9000, rms radial error=157.056, avgs=0 130/300: dt: 0.9000, rms radial error=156.182, avgs=0 135/300: dt: 0.9000, rms radial error=155.312, avgs=0 140/300: dt: 0.9000, rms radial error=154.447, avgs=0 145/300: dt: 0.9000, rms radial error=153.586, avgs=0 150/300: dt: 0.9000, rms radial error=152.730, avgs=0 155/300: dt: 0.9000, rms radial error=151.878, avgs=0 160/300: dt: 0.9000, rms radial error=151.031, avgs=0 165/300: dt: 0.9000, rms radial error=150.188, avgs=0 170/300: dt: 0.9000, rms radial error=149.350, avgs=0 175/300: dt: 0.9000, rms radial error=148.516, avgs=0 180/300: dt: 0.9000, rms radial error=147.686, avgs=0 185/300: dt: 0.9000, rms radial error=146.861, avgs=0 190/300: dt: 0.9000, rms radial error=146.041, avgs=0 195/300: dt: 0.9000, rms radial error=145.224, avgs=0 200/300: dt: 0.9000, rms radial error=144.412, avgs=0 205/300: dt: 0.9000, rms radial error=143.605, avgs=0 210/300: dt: 0.9000, rms radial error=142.802, avgs=0 215/300: dt: 0.9000, rms radial error=142.003, avgs=0 220/300: dt: 0.9000, rms radial error=141.208, avgs=0 225/300: dt: 0.9000, rms radial error=140.418, avgs=0 230/300: dt: 0.9000, rms radial error=139.632, avgs=0 235/300: dt: 0.9000, rms radial error=138.850, avgs=0 240/300: dt: 0.9000, rms radial error=138.073, avgs=0 245/300: dt: 0.9000, rms radial error=137.300, avgs=0 250/300: dt: 0.9000, rms radial error=136.531, avgs=0 255/300: dt: 0.9000, rms radial error=135.766, avgs=0 260/300: dt: 0.9000, rms radial error=135.005, avgs=0 265/300: dt: 0.9000, rms radial error=134.249, avgs=0 270/300: dt: 0.9000, rms radial error=133.496, avgs=0 275/300: dt: 0.9000, rms radial error=132.748, avgs=0 280/300: dt: 0.9000, rms radial error=132.004, avgs=0 285/300: dt: 0.9000, rms radial error=131.264, avgs=0 290/300: dt: 0.9000, rms radial error=130.528, avgs=0 295/300: dt: 0.9000, rms radial error=129.796, avgs=0 300/300: dt: 0.9000, rms radial error=129.068, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11319.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00030 epoch 2 (K=40.0), pass 1, starting sse = 1809.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 199.53 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/13 = 0.00881 epoch 4 (K=640.0), pass 1, starting sse = 16.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.33/16 = 0.02059 final distance error %29.11 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 170.714683 mris_sphere stimesec 0.259979 mris_sphere ru_maxrss 133448 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 62478 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1304 mris_sphere ru_oublock 6960 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 87 mris_sphere ru_nivcsw 495 FSRUNTIME@ mris_sphere 0.0475 hours 1 threads #-------------------------------------------- #@# Fix Topology lh Wed Nov 30 22:15:16 CET 2022 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Luce 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=-2 (nv=98856, nf=197716, ne=296574, g=2) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 1750 ambiguous faces found in tessellation segmenting defects... 5 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 5 defects to be corrected 0 vertices coincident reading input surface /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2344 (-4.6172) -vertex loglikelihood: -6.7351 (-3.3675) -normal dot loglikelihood: -3.5612 (-3.5612) -quad curv loglikelihood: -5.7755 (-2.8878) Total Loglikelihood : -25.3061 CORRECTING DEFECT 0 (vertices=165, convex hull=101, v0=1056) After retessellation of defect 0 (v0=1056), euler #=-2 (97889,293441,195550) : difference with theory (-2) = 0 CORRECTING DEFECT 1 (vertices=116, convex hull=85, v0=3906) After retessellation of defect 1 (v0=3906), euler #=-1 (97905,293529,195623) : difference with theory (-1) = 0 CORRECTING DEFECT 2 (vertices=639, convex hull=232, v0=5780) After retessellation of defect 2 (v0=5780), euler #=0 (98088,294198,196110) : difference with theory (0) = 0 CORRECTING DEFECT 3 (vertices=26, convex hull=71, v0=74662) After retessellation of defect 3 (v0=74662), euler #=1 (98097,294252,196156) : difference with theory (1) = 0 CORRECTING DEFECT 4 (vertices=47, convex hull=84, v0=80285) After retessellation of defect 4 (v0=80285), euler #=2 (98123,294363,196242) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.22 (0.10-->8.09) (max @ vno 6970 --> 98216) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.22 (0.10-->8.09) (max @ vno 6970 --> 98216) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 18 mutations (28.6%), 45 crossovers (71.4%), 56 vertices were eliminated building final representation... 733 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=98123, nf=196242, ne=294363, g=0) writing corrected surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 4.1 minutes 0 defective edges removing intersecting faces 000: 53 intersecting 001: 8 intersecting 002: 2 intersecting mris_fix_topology utimesec 242.701588 mris_fix_topology stimesec 0.227971 mris_fix_topology ru_maxrss 321784 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 79132 mris_fix_topology ru_majflt 8 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1208 mris_fix_topology ru_oublock 9232 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 281 mris_fix_topology ru_nivcsw 696 FSRUNTIME@ mris_fix_topology lh 0.0675 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 98123 - 294363 + 196242 = 2 --> 0 holes F =2V-4: 196242 = 196246-4 (0) 2E=3F: 588726 = 588726 (0) total defect index = 0 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 9 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Nov 30 22:19:23 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_make_surfaces -noaseg -noaparc -mgz -T1 brain.finalsurfs Luce lh not using aseg volume 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 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/filled.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/brain.finalsurfs.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/wm.mgz... 27605 bright wm thresholded. 111 bright non-wm voxels segmented. reading original surface position from /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.orig... computing class statistics... border white: 170670 voxels (1.02%) border gray 200740 voxels (1.20%) WM (99.0): 98.7 +- 8.5 [70.0 --> 110.0] GM (78.0) : 77.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.5 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 54.0 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.86 +- 0.22 (0.04-->6.20) (max @ vno 97947 --> 98065) face area 0.31 +- 0.14 (0.00-->10.89) mean absolute distance = 0.91 +- 1.29 3385 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=103+-7.0, GM=75+-8.7 mean inside = 95.1, mean outside = 79.0 smoothing surface for 5 iterations... mean border=84.0, 753 (753) missing vertices, mean dist 0.3 [1.2 (%26.8)->0.8 (%73.2))] %65 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, 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 (0.02-->6.27) (max @ vno 97947 --> 98065) face area 0.31 +- 0.15 (0.00-->9.77) mean absolute distance = 0.50 +- 0.76 5089 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3000204.5, rms=11.412 001: dt: 0.5000, sse=1797506.4, rms=8.311 (27.173%) 002: dt: 0.5000, sse=1270371.4, rms=6.501 (21.771%) 003: dt: 0.5000, sse=1036888.8, rms=5.514 (15.181%) 004: dt: 0.5000, sse=956721.8, rms=5.119 (7.168%) 005: dt: 0.5000, sse=934331.4, rms=5.030 (1.734%) rms = 5.03, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=936817.2, rms=5.026 (0.092%) 007: dt: 0.2500, sse=845269.0, rms=4.488 (10.692%) 008: dt: 0.2500, sse=812216.5, rms=4.297 (4.258%) 009: dt: 0.2500, sse=783970.9, rms=4.120 (4.123%) 010: dt: 0.2500, sse=751172.9, rms=3.907 (5.175%) 011: dt: 0.2500, sse=719168.1, rms=3.689 (5.580%) 012: dt: 0.2500, sse=692290.5, rms=3.501 (5.106%) 013: dt: 0.2500, sse=673620.9, rms=3.356 (4.133%) 014: dt: 0.2500, sse=657960.1, rms=3.235 (3.607%) 015: dt: 0.2500, sse=646964.0, rms=3.127 (3.325%) 016: dt: 0.2500, sse=633214.5, rms=3.030 (3.113%) 017: dt: 0.2500, sse=623499.9, rms=2.946 (2.774%) 018: dt: 0.2500, sse=614915.1, rms=2.858 (2.993%) 019: dt: 0.2500, sse=605520.4, rms=2.782 (2.638%) 020: dt: 0.2500, sse=600681.2, rms=2.718 (2.327%) 021: dt: 0.2500, sse=593506.1, rms=2.663 (2.015%) rms = 2.61, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=589005.5, rms=2.614 (1.839%) rms = 2.58, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=584713.6, rms=2.577 (1.409%) positioning took 1.5 minutes mean border=87.9, 753 (292) missing vertices, mean dist -0.4 [0.6 (%78.7)->0.3 (%21.3))] %85 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, 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 0.92 +- 0.26 (0.09-->6.68) (max @ vno 97947 --> 98065) face area 0.36 +- 0.19 (0.00-->12.26) mean absolute distance = 0.23 +- 0.47 2507 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1233619.8, rms=6.006 024: dt: 0.5000, sse=944484.8, rms=4.531 (24.562%) 025: dt: 0.5000, sse=862215.7, rms=4.133 (8.785%) 026: dt: 0.5000, sse=853231.3, rms=4.010 (2.972%) 027: dt: 0.5000, sse=827096.1, rms=3.941 (1.727%) 028: dt: 0.5000, sse=812023.2, rms=3.846 (2.411%) 029: dt: 0.5000, sse=798330.6, rms=3.782 (1.659%) 030: dt: 0.5000, sse=786207.5, rms=3.700 (2.170%) rms = 3.69, time step reduction 1 of 3 to 0.250... 031: dt: 0.5000, sse=782861.9, rms=3.691 (0.246%) 032: dt: 0.2500, sse=668535.3, rms=2.685 (27.267%) 033: dt: 0.2500, sse=647960.8, rms=2.486 (7.413%) rms = 2.45, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=656998.2, rms=2.449 (1.472%) rms = 2.40, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=641080.2, rms=2.405 (1.814%) positioning took 0.8 minutes mean border=88.7, 832 (197) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %88 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, 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 0.92 +- 0.26 (0.08-->6.69) (max @ vno 97947 --> 98065) face area 0.35 +- 0.19 (0.00-->12.31) mean absolute distance = 0.22 +- 0.38 2507 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=686665.4, rms=2.865 rms = 2.86, time step reduction 1 of 3 to 0.250... 036: dt: 0.5000, sse=690035.4, rms=2.862 (0.106%) 037: dt: 0.2500, sse=673350.1, rms=2.502 (12.589%) 038: dt: 0.2500, sse=643606.4, rms=2.413 (3.534%) rms = 2.39, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=652114.7, rms=2.391 (0.924%) rms = 2.34, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=633223.1, rms=2.343 (2.028%) positioning took 0.4 minutes mean border=89.0, 993 (165) missing vertices, mean dist -0.0 [0.3 (%52.1)->0.2 (%47.9))] %89 local maxima, % 9 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, 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 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=648521.8, rms=2.513 041: dt: 0.5000, sse=639031.5, rms=2.401 (4.479%) rms = 2.71, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=615104.6, rms=2.179 (9.249%) rms = 2.16, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=614435.5, rms=2.158 (0.961%) 044: dt: 0.1250, sse=606227.9, rms=2.078 (3.705%) rms = 2.05, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=604243.5, rms=2.049 (1.386%) positioning took 0.4 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.area vertex spacing 0.92 +- 0.26 (0.05-->6.74) (max @ vno 97947 --> 98065) face area 0.35 +- 0.20 (0.00-->12.33) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=57.7, 322 (322) missing vertices, mean dist 3.9 [1.4 (%0.2)->4.4 (%99.8))] %45 local maxima, %44 large gradients and %11 min vals, 189 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=20471026.0, rms=31.971 001: dt: 0.0500, sse=18128004.0, rms=30.040 (6.040%) 002: dt: 0.0500, sse=16437311.0, rms=28.565 (4.908%) 003: dt: 0.0500, sse=15155010.0, rms=27.394 (4.100%) 004: dt: 0.0500, sse=14137222.0, rms=26.427 (3.529%) 005: dt: 0.0500, sse=13296529.0, rms=25.601 (3.126%) 006: dt: 0.0500, sse=12584437.0, rms=24.880 (2.817%) 007: dt: 0.0500, sse=11970459.0, rms=24.241 (2.568%) 008: dt: 0.0500, sse=11432320.0, rms=23.667 (2.369%) 009: dt: 0.0500, sse=10956060.0, rms=23.147 (2.198%) 010: dt: 0.0500, sse=10531959.0, rms=22.673 (2.045%) positioning took 0.6 minutes mean border=57.4, 191 (86) missing vertices, mean dist 3.4 [0.4 (%0.7)->3.7 (%99.3))] %46 local maxima, %45 large gradients and % 9 min vals, 143 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11272502.0, rms=23.442 011: dt: 0.0500, sse=10884170.0, rms=23.015 (1.820%) 012: dt: 0.0500, sse=10537669.0, rms=22.628 (1.683%) 013: dt: 0.0500, sse=10226370.0, rms=22.274 (1.564%) 014: dt: 0.0500, sse=9947977.0, rms=21.953 (1.443%) 015: dt: 0.0500, sse=9699059.0, rms=21.661 (1.327%) 016: dt: 0.0500, sse=9477315.0, rms=21.398 (1.214%) 017: dt: 0.0500, sse=9278460.0, rms=21.160 (1.115%) 018: dt: 0.0500, sse=9101114.0, rms=20.944 (1.017%) 019: dt: 0.0500, sse=8941898.0, rms=20.749 (0.932%) 020: dt: 0.0500, sse=8799325.0, rms=20.573 (0.850%) positioning took 0.6 minutes mean border=57.4, 187 (55) missing vertices, mean dist 3.0 [0.2 (%1.6)->3.3 (%98.4))] %46 local maxima, %45 large gradients and % 9 min vals, 120 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8837295.0, rms=20.611 021: dt: 0.0500, sse=8702047.0, rms=20.442 (0.817%) 022: dt: 0.0500, sse=8582363.0, rms=20.292 (0.735%) 023: dt: 0.0500, sse=8473091.0, rms=20.154 (0.681%) 024: dt: 0.0500, sse=8373835.0, rms=20.027 (0.627%) 025: dt: 0.0500, sse=8282213.5, rms=19.910 (0.586%) 026: dt: 0.0500, sse=8197063.5, rms=19.800 (0.552%) 027: dt: 0.0500, sse=8116635.0, rms=19.696 (0.527%) 028: dt: 0.0500, sse=8039293.5, rms=19.595 (0.512%) 029: dt: 0.0500, sse=7963884.0, rms=19.496 (0.505%) 030: dt: 0.0500, sse=7890120.5, rms=19.398 (0.499%) positioning took 0.6 minutes mean border=57.4, 197 (46) missing vertices, mean dist 2.6 [0.2 (%2.9)->3.0 (%97.1))] %46 local maxima, %45 large gradients and % 9 min vals, 122 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_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 = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7924267.0, rms=19.435 031: dt: 0.5000, sse=7432032.0, rms=18.777 (3.389%) 032: dt: 0.5000, sse=6852597.0, rms=17.965 (4.322%) 033: dt: 0.5000, sse=6273900.0, rms=17.119 (4.711%) 034: dt: 0.5000, sse=5612816.5, rms=16.094 (5.983%) 035: dt: 0.5000, sse=5009703.0, rms=15.102 (6.164%) 036: dt: 0.5000, sse=4381418.0, rms=13.992 (7.353%) 037: dt: 0.5000, sse=3867734.8, rms=13.016 (6.975%) 038: dt: 0.5000, sse=3396829.0, rms=12.048 (7.432%) 039: dt: 0.5000, sse=3051903.8, rms=11.289 (6.305%) 040: dt: 0.5000, sse=2735599.2, rms=10.539 (6.642%) 041: dt: 0.5000, sse=2493306.0, rms=9.931 (5.774%) 042: dt: 0.5000, sse=2238982.2, rms=9.244 (6.917%) 043: dt: 0.5000, sse=2050037.5, rms=8.702 (5.855%) 044: dt: 0.5000, sse=1861945.9, rms=8.124 (6.641%) 045: dt: 0.5000, sse=1735029.0, rms=7.712 (5.073%) 046: dt: 0.5000, sse=1599328.6, rms=7.243 (6.089%) 047: dt: 0.5000, sse=1521185.5, rms=6.960 (3.901%) 048: dt: 0.5000, sse=1430359.8, rms=6.613 (4.985%) 049: dt: 0.5000, sse=1387383.9, rms=6.446 (2.525%) 050: dt: 0.5000, sse=1330518.1, rms=6.210 (3.662%) 051: dt: 0.5000, sse=1310783.9, rms=6.132 (1.260%) 052: dt: 0.5000, sse=1273301.1, rms=5.968 (2.669%) rms = 5.96, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1271450.4, rms=5.965 (0.055%) 054: dt: 0.2500, sse=1072735.5, rms=4.967 (16.729%) 055: dt: 0.2500, sse=1019088.7, rms=4.687 (5.634%) rms = 4.73, time step reduction 2 of 3 to 0.125... 056: dt: 0.1250, sse=991489.7, rms=4.527 (3.426%) 057: dt: 0.1250, sse=955193.5, rms=4.304 (4.928%) 058: dt: 0.1250, sse=946557.7, rms=4.249 (1.272%) rms = 4.24, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=944637.5, rms=4.236 (0.299%) positioning took 2.1 minutes mean border=54.7, 852 (23) missing vertices, mean dist 0.2 [0.2 (%28.3)->0.4 (%71.7))] %65 local maxima, %27 large gradients and % 8 min vals, 124 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, nav=8, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1533275.8, rms=6.128 060: dt: 0.5000, sse=1496645.6, rms=5.989 (2.260%) 061: dt: 0.5000, sse=1404526.6, rms=5.605 (6.423%) rms = 5.99, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1186098.1, rms=4.433 (20.900%) 063: dt: 0.2500, sse=1145232.2, rms=4.166 (6.031%) rms = 4.25, time step reduction 2 of 3 to 0.125... 064: dt: 0.1250, sse=1113961.1, rms=3.958 (4.985%) 065: dt: 0.1250, sse=1073706.1, rms=3.673 (7.214%) 066: dt: 0.1250, sse=1061523.5, rms=3.584 (2.409%) rms = 3.55, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1056671.9, rms=3.549 (0.980%) positioning took 0.7 minutes mean border=53.1, 931 (19) missing vertices, mean dist 0.1 [0.2 (%30.7)->0.2 (%69.3))] %74 local maxima, %18 large gradients and % 7 min vals, 113 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, nav=4, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1167535.4, rms=4.347 rms = 5.62, time step reduction 1 of 3 to 0.250... 068: dt: 0.2500, sse=1081115.2, rms=3.793 (12.732%) 069: dt: 0.2500, sse=1071707.6, rms=3.724 (1.818%) rms = 3.79, time step reduction 2 of 3 to 0.125... 070: dt: 0.1250, sse=1059770.4, rms=3.639 (2.294%) 071: dt: 0.1250, sse=1044105.9, rms=3.527 (3.081%) 072: dt: 0.1250, sse=1036747.1, rms=3.475 (1.478%) rms = 3.44, time step reduction 3 of 3 to 0.062... 073: dt: 0.1250, sse=1031947.9, rms=3.441 (0.970%) positioning took 0.6 minutes mean border=52.7, 1819 (17) missing vertices, mean dist 0.0 [0.2 (%40.4)->0.2 (%59.6))] %76 local maxima, %15 large gradients and % 7 min vals, 103 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, nav=2, nbrs=2, l_surf_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 pial surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1050105.0, rms=3.579 rms = 4.41, time step reduction 1 of 3 to 0.250... 074: dt: 0.2500, sse=1026766.4, rms=3.406 (4.829%) 075: dt: 0.2500, sse=1017964.4, rms=3.356 (1.483%) rms = 3.46, time step reduction 2 of 3 to 0.125... 076: dt: 0.1250, sse=1010702.8, rms=3.297 (1.737%) 077: dt: 0.1250, sse=1002595.2, rms=3.234 (1.916%) rms = 3.19, time step reduction 3 of 3 to 0.062... 078: dt: 0.1250, sse=996564.1, rms=3.190 (1.373%) positioning took 0.5 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.area.pial vertex spacing 1.07 +- 0.50 (0.10-->6.17) (max @ vno 78067 --> 78099) face area 0.45 +- 0.37 (0.00-->9.19) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 98123 vertices processed 25000 of 98123 vertices processed 50000 of 98123 vertices processed 75000 of 98123 vertices processed 0 of 98123 vertices processed 25000 of 98123 vertices processed 50000 of 98123 vertices processed 75000 of 98123 vertices processed thickness calculation complete, 21163:28713 truncations. 22158 vertices at 0 distance 65147 vertices at 1 distance 57454 vertices at 2 distance 29700 vertices at 3 distance 12863 vertices at 4 distance 5359 vertices at 5 distance 2089 vertices at 6 distance 815 vertices at 7 distance 340 vertices at 8 distance 126 vertices at 9 distance 49 vertices at 10 distance 36 vertices at 11 distance 22 vertices at 12 distance 12 vertices at 13 distance 12 vertices at 14 distance 11 vertices at 15 distance 16 vertices at 16 distance 18 vertices at 17 distance 12 vertices at 18 distance 7 vertices at 19 distance 0 vertices at 20 distance writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/lh.thickness positioning took 11.3 minutes #-------------------------------------------- #@# Smooth2 lh Wed Nov 30 22:30:43 CET 2022 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts 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 Wed Nov 30 22:30:47 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.7 mm, total surface area = 64429 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.128 (target=0.015) step 005: RMS=0.095 (target=0.015) step 010: RMS=0.074 (target=0.015) step 015: RMS=0.062 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 23.413760 mris_inflate stimesec 0.083977 mris_inflate ru_maxrss 132048 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31267 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 328 mris_inflate ru_oublock 7672 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 224 mris_inflate ru_nivcsw 64 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 162 vertices thresholded to be in k1 ~ [-0.60 0.41], k2 ~ [-0.15 0.05] total integrated curvature = 0.548*4pi (6.892) --> 0 handles ICI = 1.6, FI = 17.5, variation=263.527 81 vertices thresholded to be in [-0.01 0.05] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 98 vertices thresholded to be in [-0.31 0.21] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.022, std = 0.038 done. #----------------------------------------- #@# Curvature Stats lh Wed Nov 30 22:32:03 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Luce 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 [ Luce/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 [ 172 ] Gb_filter = 0 WARN: S lookup min: -0.374458 WARN: S explicit min: 0.000000 vertex = 1093 #-------------------------------------------- #@# Tessellate rh Wed Nov 30 22:32:06 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mri_pretess ../mri/filled.mgz 127 ../mri/brain.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 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 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2 (out of 215331: 0.000929) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 1388 vertices, 1478 faces slice 40: 5898 vertices, 6040 faces slice 50: 12848 vertices, 13086 faces slice 60: 18821 vertices, 19040 faces slice 70: 25928 vertices, 26186 faces slice 80: 33301 vertices, 33583 faces slice 90: 42022 vertices, 42334 faces slice 100: 51190 vertices, 51490 faces slice 110: 59180 vertices, 59470 faces slice 120: 66996 vertices, 67298 faces slice 130: 73568 vertices, 73822 faces slice 140: 79905 vertices, 80139 faces slice 150: 84960 vertices, 85118 faces slice 160: 89144 vertices, 89287 faces slice 170: 93023 vertices, 93151 faces slice 180: 95833 vertices, 95934 faces slice 190: 97965 vertices, 98041 faces slice 200: 99303 vertices, 99338 faces slice 210: 99614 vertices, 99616 faces slice 220: 99614 vertices, 99616 faces slice 230: 99614 vertices, 99616 faces slice 240: 99614 vertices, 99616 faces slice 250: 99614 vertices, 99616 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 99614 voxel in cpt #1: X=-2 [v=99614,e=298848,f=199232] located at (32.838367, -27.505049, 8.674955) For the whole surface: X=-2 [v=99614,e=298848,f=199232] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Nov 30 22:32:11 CET 2022 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Nov 30 22:32:14 CET 2022 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 59546 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.107 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.067 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.052 (target=0.015) step 025: RMS=0.047 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.028 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 23.673398 mris_inflate stimesec 0.068004 mris_inflate ru_maxrss 133720 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31710 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7008 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 150 mris_inflate ru_nivcsw 52 #-------------------------------------------- #@# QSphere rh Wed Nov 30 22:32:38 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.16 +- 0.69 (0.00-->5.55) (max @ vno 47403 --> 48389) face area 0.03 +- 0.03 (-0.03-->0.36) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=178.482, avgs=0 005/300: dt: 0.9000, rms radial error=178.226, avgs=0 010/300: dt: 0.9000, rms radial error=177.678, avgs=0 015/300: dt: 0.9000, rms radial error=176.958, avgs=0 020/300: dt: 0.9000, rms radial error=176.137, avgs=0 025/300: dt: 0.9000, rms radial error=175.257, avgs=0 030/300: dt: 0.9000, rms radial error=174.344, avgs=0 035/300: dt: 0.9000, rms radial error=173.413, avgs=0 040/300: dt: 0.9000, rms radial error=172.475, avgs=0 045/300: dt: 0.9000, rms radial error=171.540, avgs=0 050/300: dt: 0.9000, rms radial error=170.605, avgs=0 055/300: dt: 0.9000, rms radial error=169.672, avgs=0 060/300: dt: 0.9000, rms radial error=168.741, avgs=0 065/300: dt: 0.9000, rms radial error=167.814, avgs=0 070/300: dt: 0.9000, rms radial error=166.890, avgs=0 075/300: dt: 0.9000, rms radial error=165.971, avgs=0 080/300: dt: 0.9000, rms radial error=165.055, avgs=0 085/300: dt: 0.9000, rms radial error=164.144, avgs=0 090/300: dt: 0.9000, rms radial error=163.237, avgs=0 095/300: dt: 0.9000, rms radial error=162.334, avgs=0 100/300: dt: 0.9000, rms radial error=161.436, avgs=0 105/300: dt: 0.9000, rms radial error=160.541, avgs=0 110/300: dt: 0.9000, rms radial error=159.652, avgs=0 115/300: dt: 0.9000, rms radial error=158.766, avgs=0 120/300: dt: 0.9000, rms radial error=157.885, avgs=0 125/300: dt: 0.9000, rms radial error=157.009, avgs=0 130/300: dt: 0.9000, rms radial error=156.138, avgs=0 135/300: dt: 0.9000, rms radial error=155.270, avgs=0 140/300: dt: 0.9000, rms radial error=154.408, avgs=0 145/300: dt: 0.9000, rms radial error=153.549, avgs=0 150/300: dt: 0.9000, rms radial error=152.695, avgs=0 155/300: dt: 0.9000, rms radial error=151.846, avgs=0 160/300: dt: 0.9000, rms radial error=151.001, avgs=0 165/300: dt: 0.9000, rms radial error=150.160, avgs=0 170/300: dt: 0.9000, rms radial error=149.324, avgs=0 175/300: dt: 0.9000, rms radial error=148.491, avgs=0 180/300: dt: 0.9000, rms radial error=147.664, avgs=0 185/300: dt: 0.9000, rms radial error=146.840, avgs=0 190/300: dt: 0.9000, rms radial error=146.021, avgs=0 195/300: dt: 0.9000, rms radial error=145.207, avgs=0 200/300: dt: 0.9000, rms radial error=144.396, avgs=0 205/300: dt: 0.9000, rms radial error=143.589, avgs=0 210/300: dt: 0.9000, rms radial error=142.787, avgs=0 215/300: dt: 0.9000, rms radial error=141.989, avgs=0 220/300: dt: 0.9000, rms radial error=141.196, avgs=0 225/300: dt: 0.9000, rms radial error=140.406, avgs=0 230/300: dt: 0.9000, rms radial error=139.621, avgs=0 235/300: dt: 0.9000, rms radial error=138.841, avgs=0 240/300: dt: 0.9000, rms radial error=138.064, avgs=0 245/300: dt: 0.9000, rms radial error=137.292, avgs=0 250/300: dt: 0.9000, rms radial error=136.524, avgs=0 255/300: dt: 0.9000, rms radial error=135.760, avgs=0 260/300: dt: 0.9000, rms radial error=135.001, avgs=0 265/300: dt: 0.9000, rms radial error=134.245, avgs=0 270/300: dt: 0.9000, rms radial error=133.494, avgs=0 275/300: dt: 0.9000, rms radial error=132.747, avgs=0 280/300: dt: 0.9000, rms radial error=132.004, avgs=0 285/300: dt: 0.9000, rms radial error=131.264, avgs=0 290/300: dt: 0.9000, rms radial error=130.529, avgs=0 295/300: dt: 0.9000, rms radial error=129.798, avgs=0 300/300: dt: 0.9000, rms radial error=129.071, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11433.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00029 epoch 2 (K=40.0), pass 1, starting sse = 1835.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 208.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00935 epoch 4 (K=640.0), pass 1, starting sse = 16.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.28/17 = 0.01635 final distance error %29.27 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 176.557935 mris_sphere stimesec 0.183981 mris_sphere ru_maxrss 134432 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 70043 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 7008 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 84 mris_sphere ru_nivcsw 450 FSRUNTIME@ mris_sphere 0.0491 hours 1 threads #-------------------------------------------- #@# Fix Topology rh Wed Nov 30 22:35:35 CET 2022 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Luce rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-2 (nv=99614, nf=199232, ne=298848, g=2) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 1753 ambiguous faces found in tessellation segmenting defects... 8 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 8 defects to be corrected 0 vertices coincident reading input surface /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2374 (-4.6187) -vertex loglikelihood: -6.8044 (-3.4022) -normal dot loglikelihood: -3.5889 (-3.5889) -quad curv loglikelihood: -5.9651 (-2.9825) Total Loglikelihood : -25.5957 CORRECTING DEFECT 0 (vertices=5, convex hull=19, v0=2002) After retessellation of defect 0 (v0=2002), euler #=-5 (98602,295540,196933) : difference with theory (-5) = 0 CORRECTING DEFECT 1 (vertices=199, convex hull=139, v0=3211) After retessellation of defect 1 (v0=3211), euler #=-4 (98636,295705,197065) : difference with theory (-4) = 0 CORRECTING DEFECT 2 (vertices=703, convex hull=229, v0=4176) After retessellation of defect 2 (v0=4176), euler #=-3 (98832,296404,197569) : difference with theory (-3) = 0 CORRECTING DEFECT 3 (vertices=12, convex hull=48, v0=7831) After retessellation of defect 3 (v0=7831), euler #=-2 (98838,296436,197596) : difference with theory (-2) = 0 CORRECTING DEFECT 4 (vertices=7, convex hull=30, v0=13257) After retessellation of defect 4 (v0=13257), euler #=-1 (98840,296451,197610) : difference with theory (-1) = 0 CORRECTING DEFECT 5 (vertices=49, convex hull=102, v0=74158) After retessellation of defect 5 (v0=74158), euler #=0 (98852,296522,197670) : difference with theory (0) = 0 CORRECTING DEFECT 6 (vertices=26, convex hull=59, v0=84506) After retessellation of defect 6 (v0=84506), euler #=1 (98861,296573,197713) : difference with theory (1) = 0 CORRECTING DEFECT 7 (vertices=11, convex hull=16, v0=98773) After retessellation of defect 7 (v0=98773), euler #=2 (98863,296583,197722) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.04-->10.28) (max @ vno 4073 --> 4937) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.04-->10.28) (max @ vno 4073 --> 4937) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 20 mutations (33.3%), 40 crossovers (66.7%), 64 vertices were eliminated building final representation... 751 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=98863, nf=197722, ne=296583, g=0) writing corrected surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 3.8 minutes 0 defective edges removing intersecting faces 000: 98 intersecting 001: 3 intersecting mris_fix_topology utimesec 230.340735 mris_fix_topology stimesec 0.191977 mris_fix_topology ru_maxrss 323728 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 79840 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 9312 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 247 mris_fix_topology ru_nivcsw 952 FSRUNTIME@ mris_fix_topology rh 0.0641 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 98863 - 296583 + 197722 = 2 --> 0 holes F =2V-4: 197722 = 197726-4 (0) 2E=3F: 593166 = 593166 (0) total defect index = 0 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 23 intersecting 001: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed Nov 30 22:39:30 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_make_surfaces -noaseg -noaparc -mgz -T1 brain.finalsurfs Luce rh not using aseg volume 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 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/filled.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/brain.finalsurfs.mgz... reading volume /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/mri/wm.mgz... 27605 bright wm thresholded. 111 bright non-wm voxels segmented. reading original surface position from /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.orig... computing class statistics... border white: 170670 voxels (1.02%) border gray 200740 voxels (1.20%) WM (99.0): 98.7 +- 8.5 [70.0 --> 110.0] GM (78.0) : 77.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.5 (was 70) setting MAX_BORDER_WHITE to 110.5 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 55.0 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.86 +- 0.22 (0.05-->5.59) (max @ vno 98771 --> 98819) face area 0.31 +- 0.14 (0.00-->6.18) mean absolute distance = 0.92 +- 1.31 3407 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=102+-7.8, GM=76+-8.7 mean inside = 95.2, mean outside = 80.0 smoothing surface for 5 iterations... mean border=84.7, 953 (953) missing vertices, mean dist 0.3 [1.2 (%26.7)->0.8 (%73.3))] %63 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.07-->5.76) (max @ vno 98692 --> 98783) face area 0.31 +- 0.15 (0.00-->5.53) mean absolute distance = 0.50 +- 0.78 4556 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2746018.2, rms=10.783 001: dt: 0.5000, sse=1656501.6, rms=7.833 (27.360%) 002: dt: 0.5000, sse=1205219.2, rms=6.206 (20.768%) 003: dt: 0.5000, sse=1018610.1, rms=5.394 (13.084%) 004: dt: 0.5000, sse=960184.6, rms=5.124 (5.012%) rms = 5.12, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=958620.2, rms=5.116 (0.157%) 006: dt: 0.2500, sse=892570.6, rms=4.729 (7.567%) 007: dt: 0.2500, sse=879590.9, rms=4.646 (1.755%) 008: dt: 0.2500, sse=858411.0, rms=4.537 (2.348%) 009: dt: 0.2500, sse=819234.9, rms=4.302 (5.169%) 010: dt: 0.2500, sse=774866.5, rms=4.033 (6.247%) 011: dt: 0.2500, sse=731083.9, rms=3.746 (7.120%) 012: dt: 0.2500, sse=699200.4, rms=3.520 (6.035%) 013: dt: 0.2500, sse=674811.9, rms=3.338 (5.181%) 014: dt: 0.2500, sse=658269.2, rms=3.208 (3.893%) 015: dt: 0.2500, sse=646502.4, rms=3.104 (3.224%) 016: dt: 0.2500, sse=636687.6, rms=3.024 (2.575%) rms = 2.98, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=631139.5, rms=2.977 (1.583%) rms = 2.94, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=626156.8, rms=2.936 (1.377%) positioning took 1.2 minutes mean border=88.3, 959 (435) missing vertices, mean dist -0.4 [0.6 (%77.2)->0.3 (%22.8))] %83 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, 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 0.92 +- 0.26 (0.12-->6.02) (max @ vno 98692 --> 98783) face area 0.36 +- 0.18 (0.00-->7.30) mean absolute distance = 0.25 +- 0.49 2974 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1204916.5, rms=5.861 019: dt: 0.5000, sse=935668.7, rms=4.528 (22.736%) 020: dt: 0.5000, sse=862749.2, rms=4.139 (8.595%) 021: dt: 0.5000, sse=842937.1, rms=4.029 (2.650%) rms = 3.99, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=837441.6, rms=3.989 (0.987%) 023: dt: 0.2500, sse=741134.5, rms=3.290 (17.542%) 024: dt: 0.2500, sse=713564.6, rms=3.058 (7.050%) 025: dt: 0.2500, sse=697046.1, rms=2.920 (4.505%) 026: dt: 0.2500, sse=691280.2, rms=2.810 (3.780%) 027: dt: 0.2500, sse=678955.1, rms=2.734 (2.703%) 028: dt: 0.2500, sse=669500.9, rms=2.671 (2.298%) 029: dt: 0.2500, sse=666317.0, rms=2.620 (1.888%) rms = 2.57, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=661317.2, rms=2.573 (1.809%) rms = 2.54, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=656886.6, rms=2.540 (1.291%) positioning took 0.8 minutes mean border=89.1, 1041 (357) missing vertices, mean dist -0.1 [0.3 (%58.6)->0.2 (%41.4))] %86 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, 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 0.92 +- 0.26 (0.05-->5.97) (max @ vno 98692 --> 98783) face area 0.36 +- 0.19 (0.00-->7.42) mean absolute distance = 0.24 +- 0.40 2886 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=709537.8, rms=3.023 032: dt: 0.5000, sse=703813.9, rms=2.940 (2.737%) rms = 3.01, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=681352.1, rms=2.697 (8.283%) 034: dt: 0.2500, sse=662599.6, rms=2.595 (3.771%) rms = 2.56, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=657848.6, rms=2.556 (1.512%) rms = 2.51, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=653140.1, rms=2.512 (1.693%) positioning took 0.4 minutes mean border=89.4, 1236 (337) missing vertices, mean dist -0.1 [0.3 (%52.0)->0.2 (%48.0))] %87 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, 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 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=670057.9, rms=2.681 037: dt: 0.5000, sse=652423.1, rms=2.530 (5.642%) rms = 2.78, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=637634.3, rms=2.354 (6.939%) rms = 2.34, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=644162.8, rms=2.344 (0.414%) 040: dt: 0.1250, sse=625983.4, rms=2.278 (2.821%) rms = 2.25, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=624921.8, rms=2.251 (1.179%) positioning took 0.4 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.area vertex spacing 0.92 +- 0.26 (0.07-->5.95) (max @ vno 98692 --> 98783) face area 0.36 +- 0.19 (0.00-->7.30) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=58.7, 350 (350) missing vertices, mean dist 3.9 [1.6 (%0.3)->4.4 (%99.7))] %47 local maxima, %42 large gradients and %11 min vals, 236 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=19850926.0, rms=31.355 001: dt: 0.0500, sse=17722442.0, rms=29.583 (5.652%) 002: dt: 0.0500, sse=16159395.0, rms=28.211 (4.638%) 003: dt: 0.0500, sse=14960698.0, rms=27.112 (3.897%) 004: dt: 0.0500, sse=13999929.0, rms=26.197 (3.373%) 005: dt: 0.0500, sse=13202620.0, rms=25.413 (2.993%) 006: dt: 0.0500, sse=12524548.0, rms=24.726 (2.701%) 007: dt: 0.0500, sse=11936737.0, rms=24.116 (2.471%) 008: dt: 0.0500, sse=11420741.0, rms=23.566 (2.278%) 009: dt: 0.0500, sse=10962716.0, rms=23.068 (2.116%) 010: dt: 0.0500, sse=10553895.0, rms=22.613 (1.970%) positioning took 0.6 minutes mean border=58.3, 214 (111) missing vertices, mean dist 3.3 [0.6 (%0.6)->3.7 (%99.4))] %48 local maxima, %43 large gradients and % 9 min vals, 185 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11346586.0, rms=23.434 011: dt: 0.0500, sse=10969805.0, rms=23.023 (1.754%) 012: dt: 0.0500, sse=10631752.0, rms=22.648 (1.629%) 013: dt: 0.0500, sse=10326516.0, rms=22.304 (1.519%) 014: dt: 0.0500, sse=10052179.0, rms=21.990 (1.407%) 015: dt: 0.0500, sse=9805702.0, rms=21.704 (1.300%) 016: dt: 0.0500, sse=9584955.0, rms=21.445 (1.195%) 017: dt: 0.0500, sse=9385147.0, rms=21.207 (1.108%) 018: dt: 0.0500, sse=9205107.0, rms=20.991 (1.020%) 019: dt: 0.0500, sse=9042435.0, rms=20.794 (0.941%) 020: dt: 0.0500, sse=8895139.0, rms=20.613 (0.868%) positioning took 0.6 minutes mean border=58.3, 205 (81) missing vertices, mean dist 3.0 [0.2 (%1.9)->3.3 (%98.1))] %48 local maxima, %43 large gradients and % 9 min vals, 189 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8942445.0, rms=20.661 021: dt: 0.0500, sse=8801615.0, rms=20.488 (0.841%) 022: dt: 0.0500, sse=8675344.0, rms=20.331 (0.767%) 023: dt: 0.0500, sse=8558728.0, rms=20.184 (0.719%) 024: dt: 0.0500, sse=8451483.0, rms=20.049 (0.671%) 025: dt: 0.0500, sse=8351577.5, rms=19.922 (0.634%) 026: dt: 0.0500, sse=8258323.0, rms=19.803 (0.599%) 027: dt: 0.0500, sse=8168958.5, rms=19.688 (0.581%) 028: dt: 0.0500, sse=8082256.0, rms=19.575 (0.571%) 029: dt: 0.0500, sse=7997641.5, rms=19.465 (0.564%) 030: dt: 0.0500, sse=7914264.0, rms=19.356 (0.562%) positioning took 0.6 minutes mean border=58.3, 202 (63) missing vertices, mean dist 2.6 [0.2 (%3.5)->3.0 (%96.5))] %48 local maxima, %43 large gradients and % 9 min vals, 182 gradients ignored tol=1.0e-04, sigma=2.0, host=gbw-d, nav=16, nbrs=2, l_surf_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 = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7954371.5, rms=19.399 031: dt: 0.5000, sse=7400082.5, rms=18.660 (3.809%) 032: dt: 0.5000, sse=6786739.5, rms=17.801 (4.605%) 033: dt: 0.5000, sse=6201722.5, rms=16.943 (4.819%) 034: dt: 0.5000, sse=5567367.5, rms=15.957 (5.818%) 035: dt: 0.5000, sse=4991304.0, rms=15.009 (5.943%) 036: dt: 0.5000, sse=4395244.5, rms=13.957 (7.007%) 037: dt: 0.5000, sse=3905042.5, rms=13.031 (6.638%) 038: dt: 0.5000, sse=3461579.2, rms=12.128 (6.927%) 039: dt: 0.5000, sse=3124381.2, rms=11.396 (6.038%) 040: dt: 0.5000, sse=2795495.2, rms=10.629 (6.727%) 041: dt: 0.5000, sse=2525234.0, rms=9.959 (6.308%) 042: dt: 0.5000, sse=2261886.5, rms=9.255 (7.065%) 043: dt: 0.5000, sse=2059405.2, rms=8.679 (6.224%) 044: dt: 0.5000, sse=1862458.5, rms=8.075 (6.958%) 045: dt: 0.5000, sse=1725341.2, rms=7.631 (5.502%) 046: dt: 0.5000, sse=1583723.2, rms=7.139 (6.452%) 047: dt: 0.5000, sse=1501982.0, rms=6.841 (4.165%) 048: dt: 0.5000, sse=1406351.2, rms=6.473 (5.386%) 049: dt: 0.5000, sse=1360863.2, rms=6.292 (2.787%) 050: dt: 0.5000, sse=1297174.6, rms=6.027 (4.212%) 051: dt: 0.5000, sse=1282045.1, rms=5.965 (1.041%) 052: dt: 0.5000, sse=1242841.5, rms=5.793 (2.873%) rms = 5.81, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1048136.8, rms=4.814 (16.895%) 054: dt: 0.2500, sse=1001333.2, rms=4.541 (5.687%) rms = 4.55, time step reduction 2 of 3 to 0.125... 055: dt: 0.1250, sse=975916.7, rms=4.390 (3.326%) 056: dt: 0.1250, sse=940533.3, rms=4.170 (5.013%) 057: dt: 0.1250, sse=931479.1, rms=4.111 (1.400%) rms = 4.10, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=929189.2, rms=4.096 (0.372%) positioning took 2.1 minutes mean border=55.5, 884 (29) missing vertices, mean dist 0.2 [0.2 (%27.6)->0.4 (%72.4))] %66 local maxima, %25 large gradients and % 8 min vals, 189 gradients ignored tol=1.0e-04, sigma=1.0, host=gbw-d, nav=8, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1542052.8, rms=6.105 059: dt: 0.5000, sse=1494818.9, rms=5.924 (2.967%) 060: dt: 0.5000, sse=1405267.2, rms=5.550 (6.315%) rms = 5.90, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1186609.6, rms=4.372 (21.223%) 062: dt: 0.2500, sse=1140799.0, rms=4.074 (6.818%) rms = 4.17, time step reduction 2 of 3 to 0.125... 063: dt: 0.1250, sse=1110526.6, rms=3.869 (5.029%) 064: dt: 0.1250, sse=1070911.8, rms=3.582 (7.419%) 065: dt: 0.1250, sse=1059570.0, rms=3.498 (2.351%) rms = 3.47, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1055430.9, rms=3.467 (0.877%) positioning took 0.7 minutes mean border=53.9, 984 (24) missing vertices, mean dist 0.1 [0.2 (%29.5)->0.2 (%70.5))] %75 local maxima, %16 large gradients and % 8 min vals, 139 gradients ignored tol=1.0e-04, sigma=0.5, host=gbw-d, nav=4, nbrs=2, l_surf_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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1159225.2, rms=4.233 rms = 5.49, time step reduction 1 of 3 to 0.250... 067: dt: 0.2500, sse=1078137.8, rms=3.703 (12.517%) 068: dt: 0.2500, sse=1065578.6, rms=3.611 (2.486%) rms = 3.69, time step reduction 2 of 3 to 0.125... 069: dt: 0.1250, sse=1055327.4, rms=3.536 (2.093%) 070: dt: 0.1250, sse=1041573.1, rms=3.434 (2.870%) rms = 3.39, time step reduction 3 of 3 to 0.062... 071: dt: 0.1250, sse=1035099.4, rms=3.387 (1.379%) positioning took 0.5 minutes mean border=53.5, 1894 (22) missing vertices, mean dist 0.0 [0.2 (%39.8)->0.2 (%60.2))] %77 local maxima, %14 large gradients and % 7 min vals, 137 gradients ignored tol=1.0e-04, sigma=0.2, host=gbw-d, nav=2, nbrs=2, l_surf_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 pial surface to /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1054426.1, rms=3.538 rms = 4.33, time step reduction 1 of 3 to 0.250... 072: dt: 0.2500, sse=1031266.9, rms=3.366 (4.856%) 073: dt: 0.2500, sse=1022037.9, rms=3.312 (1.614%) rms = 3.41, time step reduction 2 of 3 to 0.125... 074: dt: 0.1250, sse=1015244.2, rms=3.257 (1.665%) 075: dt: 0.1250, sse=1006478.9, rms=3.188 (2.127%) rms = 3.15, time step reduction 3 of 3 to 0.062... 076: dt: 0.1250, sse=1001420.1, rms=3.150 (1.168%) positioning took 0.5 minutes writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.area.pial vertex spacing 1.07 +- 0.51 (0.08-->6.10) (max @ vno 82135 --> 82143) face area 0.45 +- 0.37 (0.00-->7.52) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 98863 vertices processed 25000 of 98863 vertices processed 50000 of 98863 vertices processed 75000 of 98863 vertices processed 0 of 98863 vertices processed 25000 of 98863 vertices processed 50000 of 98863 vertices processed 75000 of 98863 vertices processed thickness calculation complete, 22323:29306 truncations. 22619 vertices at 0 distance 64970 vertices at 1 distance 57874 vertices at 2 distance 30367 vertices at 3 distance 13051 vertices at 4 distance 5327 vertices at 5 distance 2026 vertices at 6 distance 828 vertices at 7 distance 326 vertices at 8 distance 138 vertices at 9 distance 79 vertices at 10 distance 28 vertices at 11 distance 17 vertices at 12 distance 10 vertices at 13 distance 9 vertices at 14 distance 16 vertices at 15 distance 13 vertices at 16 distance 10 vertices at 17 distance 2 vertices at 18 distance 6 vertices at 19 distance 10 vertices at 20 distance writing curvature file /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf/rh.thickness positioning took 11.0 minutes #-------------------------------------------- #@# Smooth2 rh Wed Nov 30 22:50:31 CET 2022 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Nov 30 22:50:35 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.1 mm, total surface area = 64880 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.130 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.075 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.049 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 23.533049 mris_inflate stimesec 0.075964 mris_inflate ru_maxrss 132824 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31490 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 96 mris_inflate ru_oublock 7736 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 198 mris_inflate ru_nivcsw 68 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 139 vertices thresholded to be in k1 ~ [-0.52 0.33], k2 ~ [-0.13 0.08] total integrated curvature = 0.578*4pi (7.259) --> 0 handles ICI = 1.6, FI = 17.2, variation=261.003 73 vertices thresholded to be in [-0.01 0.04] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 90 vertices thresholded to be in [-0.26 0.17] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.021, std = 0.037 done. #----------------------------------------- #@# Curvature Stats rh Wed Nov 30 22:51:51 CET 2022 /mnt/.autofs/storage/gbw-s-neu01_fmri-monkey-raw/fs/subjects/Luce/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Luce rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Luce/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 180 ] Gb_filter = 0 #------------------------------------------ Started at Wed Nov 30 22:11:36 CET 2022 Ended at Wed Nov 30 22:51:54 CET 2022 #@#%# recon-all-run-time-hours 0.672 recon-all -s Luce finished without error at Wed Nov 30 22:51:54 CET 2022