Thu Oct 26 21:16:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050418 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 1 subjid 0050418 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Actual FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux tars-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse 10485760 kbytes vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 65993348 61670368 4322980 2171432 0 59689464 -/+ buffers/cache: 1980904 64012444 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:50-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:51-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:52-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-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: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/26-19:16:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: ntraut Machine: tars-623 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_2/0050418/session_1/anat_1/mprage.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 26 21:16:55 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 26 21:17:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux tars-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 26 21:17:03 CEST 2017 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 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9207 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9207/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9207/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9207/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 26 21:17:05 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9207/nu0.mnc ./tmp.mri_nu_correct.mni.9207/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9207/0/ -iterations 1000 -distance 50 [ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/] [2017-10-26 21:17:05] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9207/0/ ./tmp.mri_nu_correct.mni.9207/nu0.mnc ./tmp.mri_nu_correct.mni.9207/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 Number of iterations: 30 CV of field change: 0.000966525 mri_convert ./tmp.mri_nu_correct.mni.9207/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9207/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.9207/nu1.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 changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Oct 26 21:18:06 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Oct 26 21:18:06 CEST 2017 Ended at Thu Oct 26 21:18:49 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 26 21:18:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7729, pval=0.6675 >= threshold=0.0050) awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach_avi.log TalAviQA: 0.97571 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 26 21:18:51 CEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux tars-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 26 21:18:51 CEST 2017 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 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10482 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10482/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10482/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10482/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 26 21:18:54 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10482/nu0.mnc ./tmp.mri_nu_correct.mni.10482/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10482/0/ [ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/] [2017-10-26 21:18:54] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10482/0/ ./tmp.mri_nu_correct.mni.10482/nu0.mnc ./tmp.mri_nu_correct.mni.10482/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 Number of iterations: 23 CV of field change: 0.000970842 -------------------------------------------------------- Iteration 2 Thu Oct 26 21:19:39 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10482/nu1.mnc ./tmp.mri_nu_correct.mni.10482/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10482/1/ [ntraut@tars-623:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/] [2017-10-26 21:19:39] running: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10482/1/ ./tmp.mri_nu_correct.mni.10482/nu1.mnc ./tmp.mri_nu_correct.mni.10482/nu2.imp 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: 11 CV of field change: 0.000962955 mri_binarize --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10482/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10482/ones.mgz sysname Linux hostname tars-623 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.10482/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10482/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/input.mean.dat sysname Linux hostname tars-623 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10482/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.10482/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10482/ones.mgz --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10482/ones.mgz --i ./tmp.mri_nu_correct.mni.10482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10482/output.mean.dat sysname Linux hostname tars-623 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10482/ones.mgz Loading ./tmp.mri_nu_correct.mni.10482/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.10482/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10482/nu2.mnc ./tmp.mri_nu_correct.mni.10482/nu2.mnc mul 1.02006471169111547311 Saving result to './tmp.mri_nu_correct.mni.10482/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10482/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10482/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.10482/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 9 seconds. mapping (18, 98) to ( 3, 110) Thu Oct 26 21:21:01 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Oct 26 21:21:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.04097 -0.04239 -0.06629 -5.29266; 0.00666 1.05572 0.17579 -1.07414; 0.07116 -0.20519 1.08700 -8.95361; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 13 Starting OpenSpline(): npoints = 13 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 66 (66), valley at 30 (30) csf peak at 34, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 63 (63), valley at 19 (19) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 20 seconds. #-------------------------------------------- #@# Skull Stripping Thu Oct 26 21:23:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (51, 40, 18) --> (199, 192, 210) using (100, 91, 114) as brain centroid... mean wm in atlas = 108, using box (82,72,90) --> (118, 109,137) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 101 +- 7.4 after smoothing, mri peak at 101, scaling input intensities by 1.069 scaling channel 0 by 1.06931 initial log_p = -4.380 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.475875 @ (0.000, 0.000, 0.000) max log p = -4.434344 @ (4.545, 4.545, -4.545) max log p = -4.386528 @ (2.273, -6.818, 2.273) max log p = -4.350627 @ (-3.409, -1.136, 1.136) max log p = -4.328517 @ (-0.568, 6.250, -3.977) max log p = -4.328517 @ (0.000, 0.000, 0.000) Found translation: (2.8, 2.8, -5.1): log p = -4.329 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.169, old_max_log_p =-4.329 (thresh=-4.3) 0.99144 -0.01959 0.12941 -8.40144; 0.00000 1.22567 0.14032 -37.38474; -0.14032 -0.15998 1.05669 27.72302; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.169, old_max_log_p =-4.169 (thresh=-4.2) 0.99144 -0.01959 0.12941 -8.40144; 0.00000 1.22567 0.14032 -37.38474; -0.14032 -0.15998 1.05669 27.72302; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.093, old_max_log_p =-4.169 (thresh=-4.2) 1.01829 -0.05325 0.02250 6.74322; 0.03572 1.16061 0.10545 -32.60637; -0.04825 -0.12769 1.12894 5.93081; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.093, old_max_log_p =-4.093 (thresh=-4.1) 1.01829 -0.05325 0.02250 6.74322; 0.03572 1.16061 0.10545 -32.60637; -0.04825 -0.12769 1.12894 5.93081; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.071, old_max_log_p =-4.093 (thresh=-4.1) 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.071, old_max_log_p =-4.071 (thresh=-4.1) 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.071 (old=-4.380) transform before final EM align: 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.5 tol 0.000000 final transform: 1.01710 -0.05319 0.02247 7.35184; 0.03560 1.15653 0.10508 -31.99239; -0.04836 -0.12799 1.13158 5.68473; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1137.771032 mri_em_register stimesec 1.124829 mri_em_register ru_maxrss 609804 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 160654 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 53 mri_em_register ru_nivcsw 3136 registration took 18 minutes and 58 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=120 y=110 z=112 r=68 first estimation of the main basin volume: 1353111 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=93, y=104, z=79, 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 10 percent done. Analyze... main basin size=7658985528 voxels, voxel volume =1.000 = 7658985528 mmm3 = 7658985.472 cm3 done. PostAnalyze...Basin Prior 284 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin ambiguous basin, non merged: 1 ambiguous voxels; size: 2913 voxels done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=121,y=116, z=105, r=8954 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 45063 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1035607993 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1045139458 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1087311690 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1066026468 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1079567910 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 4, 35, 56 after analyzing : 3, 24, 35, 32 RIGHT_CER before analyzing : 3, 4, 37, 67 after analyzing : 3, 26, 37, 36 LEFT_CER before analyzing : 3, 5, 41, 57 after analyzing : 3, 29, 41, 36 RIGHT_BRAIN before analyzing : 3, 4, 36, 56 after analyzing : 3, 25, 36, 32 LEFT_BRAIN before analyzing : 3, 4, 33, 56 after analyzing : 3, 23, 33, 31 OTHER before analyzing : 4, 6, 35, 56 after analyzing : 4, 25, 35, 32 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 70.554, std = 7.207 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.65, sigma = 3.85 after rotation: sse = 2.65, sigma = 3.85 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.85, its var is 3.74 before Erosion-Dilatation 0.34% of inacurate vertices after Erosion-Dilatation 0.00% 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...32 iterations mri_strip_skull: done peeling brain Brain Size = 1625863 voxels, voxel volume = 1.000 mm3 = 1625863 mmm3 = 1625.863 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 21.064797 mri_watershed stimesec 0.482926 mri_watershed ru_maxrss 818700 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 210377 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 7552 mri_watershed ru_oublock 2592 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 154 mri_watershed ru_nivcsw 123 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Oct 26 21:42:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.0 skull bounding box = (52, 57, 33) --> (191, 183, 188) using (98, 99, 111) as brain centroid... mean wm in atlas = 107, using box (81,84,92) --> (115, 114,130) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 7.5 after smoothing, mri peak at 100, scaling input intensities by 1.070 scaling channel 0 by 1.07 initial log_p = -3.974 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.070300 @ (0.000, 0.000, 0.000) max log p = -3.935298 @ (4.545, 4.545, -4.545) max log p = -3.921781 @ (-2.273, -2.273, 2.273) max log p = -3.861459 @ (1.136, 1.136, -1.136) max log p = -3.859510 @ (-0.568, -1.705, 0.568) max log p = -3.857513 @ (-0.284, -1.989, -0.284) Found translation: (2.6, -0.3, -3.1): log p = -3.858 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.858, old_max_log_p =-3.858 (thresh=-3.9) 1.00000 0.00000 0.00000 2.55682; 0.00000 1.00000 0.00000 -0.28409; 0.00000 0.00000 1.00000 -3.12500; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.764, old_max_log_p =-3.858 (thresh=-3.9) 1.01803 -0.00377 -0.00461 3.11295; 0.00424 1.05436 0.07392 -11.76360; 0.00442 -0.07258 1.03495 3.31443; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.756, old_max_log_p =-3.764 (thresh=-3.8) 1.05170 -0.08035 0.06030 1.00317; 0.07334 1.09098 0.08081 -25.21089; -0.05984 -0.06947 0.99430 15.13697; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.756, old_max_log_p =-3.756 (thresh=-3.8) 1.05170 -0.08035 0.06030 1.00317; 0.07334 1.09098 0.08081 -25.21089; -0.05984 -0.06947 0.99430 15.13697; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.729, old_max_log_p =-3.756 (thresh=-3.8) 1.04673 -0.10560 0.04192 6.97104; 0.09913 1.08872 0.08160 -28.18139; -0.04251 -0.07041 0.99401 12.67247; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.728, old_max_log_p =-3.729 (thresh=-3.7) 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.728 (old=-3.974) transform before final EM align: 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000 final transform: 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 954.697863 mri_em_register stimesec 0.732888 mri_em_register ru_maxrss 599032 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158993 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 85 mri_em_register ru_nivcsw 2063 registration took 15 minutes and 55 seconds. #-------------------------------------- #@# CA Normalize Thu Oct 26 21:58:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.0 skull bounding box = (52, 57, 33) --> (191, 183, 188) using (98, 99, 111) as brain centroid... mean wm in atlas = 107, using box (81,84,92) --> (115, 114,130) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 7.5 after smoothing, mri peak at 100, scaling input intensities by 1.070 scaling channel 0 by 1.07 using 246344 sample points... INFO: compute sample coordinates transform 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18139; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 54, 28) --> (186, 160, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 251 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (59, 57, 27) --> (122, 166, 196) Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 132.0 23 of 167 (13.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 135, 53) --> (175, 172, 107) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 136, 49) --> (127, 175, 108) Right_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 0 of 18 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 126, 88) --> (143, 191, 119) Brain_Stem: limiting intensities to 93.0 --> 132.0 3 of 17 (17.6%) samples deleted using 462 total control points for intensity normalization... bias field = 0.963 +- 0.096 0 of 436 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 54, 28) --> (186, 160, 197) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 119 of 368 (32.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (59, 57, 27) --> (122, 166, 196) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 352 (1.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 135, 53) --> (175, 172, 107) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 37 of 40 (92.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 136, 49) --> (127, 175, 108) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 54 (46.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 126, 88) --> (143, 191, 119) Brain_Stem: limiting intensities to 88.0 --> 132.0 79 of 86 (91.9%) samples deleted using 900 total control points for intensity normalization... bias field = 1.012 +- 0.068 0 of 636 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 54, 28) --> (186, 160, 197) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 454 (3.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (59, 57, 27) --> (122, 166, 196) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 422 (0.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 135, 53) --> (175, 172, 107) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 64 of 80 (80.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 136, 49) --> (127, 175, 108) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 53 (77.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 126, 88) --> (143, 191, 119) Brain_Stem: limiting intensities to 88.0 --> 91.0 129 of 129 (100.0%) samples deleted using 1138 total control points for intensity normalization... bias field = 1.043 +- 0.068 0 of 831 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 44 seconds. #-------------------------------------- #@# CA Reg Thu Oct 26 22:00:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.15 (predicted orig area = 7.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.940, neg=0, invalid=762 0001: dt=362.101792, rms=0.833 (11.405%), neg=0, invalid=762 0002: dt=262.080903, rms=0.799 (4.070%), neg=0, invalid=762 0003: dt=271.508714, rms=0.787 (1.563%), neg=0, invalid=762 0004: dt=182.436782, rms=0.781 (0.768%), neg=0, invalid=762 0005: dt=517.888000, rms=0.774 (0.826%), neg=0, invalid=762 0006: dt=129.472000, rms=0.772 (0.297%), neg=0, invalid=762 0007: dt=2071.552000, rms=0.763 (1.113%), neg=0, invalid=762 0008: dt=129.472000, rms=0.762 (0.164%), neg=0, invalid=762 0009: dt=129.472000, rms=0.761 (0.109%), neg=0, invalid=762 0010: dt=129.472000, rms=0.760 (0.173%), neg=0, invalid=762 0011: dt=129.472000, rms=0.758 (0.194%), neg=0, invalid=762 0012: dt=129.472000, rms=0.757 (0.193%), neg=0, invalid=762 0013: dt=129.472000, rms=0.755 (0.190%), neg=0, invalid=762 0014: dt=129.472000, rms=0.754 (0.201%), neg=0, invalid=762 0015: dt=129.472000, rms=0.752 (0.214%), neg=0, invalid=762 0016: dt=129.472000, rms=0.751 (0.186%), neg=0, invalid=762 0017: dt=129.472000, rms=0.750 (0.185%), neg=0, invalid=762 0018: dt=129.472000, rms=0.748 (0.198%), neg=0, invalid=762 0019: dt=129.472000, rms=0.747 (0.203%), neg=0, invalid=762 0020: dt=129.472000, rms=0.745 (0.178%), neg=0, invalid=762 0021: dt=129.472000, rms=0.744 (0.142%), neg=0, invalid=762 0022: dt=129.472000, rms=0.743 (0.127%), neg=0, invalid=762 0023: dt=129.472000, rms=0.742 (0.110%), neg=0, invalid=762 0024: dt=129.472000, rms=0.742 (0.096%), neg=0, invalid=762 0025: dt=1183.744000, rms=0.741 (0.125%), neg=0, invalid=762 0026: dt=110.976000, rms=0.740 (0.043%), neg=0, invalid=762 0027: dt=110.976000, rms=0.740 (0.031%), neg=0, invalid=762 0028: dt=110.976000, rms=0.740 (0.032%), neg=0, invalid=762 0029: dt=110.976000, rms=0.740 (0.042%), neg=0, invalid=762 0030: dt=110.976000, rms=0.739 (0.042%), neg=0, invalid=762 0031: dt=110.976000, rms=0.739 (0.048%), neg=0, invalid=762 0032: dt=110.976000, rms=0.739 (0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.739, neg=0, invalid=762 0033: dt=221.952000, rms=0.737 (0.223%), neg=0, invalid=762 0034: dt=517.888000, rms=0.737 (0.097%), neg=0, invalid=762 0035: dt=517.888000, rms=0.737 (-0.034%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.743, neg=0, invalid=762 0036: dt=132.977778, rms=0.736 (0.871%), neg=0, invalid=762 0037: dt=160.619355, rms=0.729 (1.017%), neg=0, invalid=762 0038: dt=67.727121, rms=0.725 (0.589%), neg=0, invalid=762 0039: dt=497.664000, rms=0.715 (1.309%), neg=0, invalid=762 0040: dt=76.000000, rms=0.710 (0.730%), neg=0, invalid=762 0041: dt=94.635071, rms=0.708 (0.281%), neg=0, invalid=762 0042: dt=65.523810, rms=0.707 (0.144%), neg=0, invalid=762 0043: dt=65.523810, rms=0.706 (0.136%), neg=0, invalid=762 0044: dt=65.523810, rms=0.704 (0.220%), neg=0, invalid=762 0045: dt=65.523810, rms=0.702 (0.306%), neg=0, invalid=762 0046: dt=65.523810, rms=0.700 (0.348%), neg=0, invalid=762 0047: dt=65.523810, rms=0.697 (0.379%), neg=0, invalid=762 0048: dt=65.523810, rms=0.694 (0.398%), neg=0, invalid=762 0049: dt=65.523810, rms=0.692 (0.366%), neg=0, invalid=762 0050: dt=65.523810, rms=0.689 (0.351%), neg=0, invalid=762 0051: dt=65.523810, rms=0.687 (0.299%), neg=0, invalid=762 0052: dt=65.523810, rms=0.685 (0.276%), neg=0, invalid=762 0053: dt=65.523810, rms=0.684 (0.237%), neg=0, invalid=762 0054: dt=65.523810, rms=0.682 (0.218%), neg=0, invalid=762 0055: dt=65.523810, rms=0.681 (0.187%), neg=0, invalid=762 0056: dt=65.523810, rms=0.680 (0.154%), neg=0, invalid=762 0057: dt=65.523810, rms=0.679 (0.123%), neg=0, invalid=762 0058: dt=65.523810, rms=0.678 (0.109%), neg=0, invalid=762 0059: dt=124.416000, rms=0.678 (0.040%), neg=0, invalid=762 0060: dt=124.416000, rms=0.678 (-0.112%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0061: dt=65.991111, rms=0.677 (0.261%), neg=0, invalid=762 0062: dt=145.152000, rms=0.676 (0.140%), neg=0, invalid=762 0063: dt=145.152000, rms=0.676 (-0.086%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0064: dt=4.800000, rms=0.704 (0.132%), neg=0, invalid=762 0065: dt=2.000000, rms=0.704 (0.008%), neg=0, invalid=762 0066: dt=2.000000, rms=0.704 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0067: dt=0.175000, rms=0.704 (0.084%), neg=0, invalid=762 0068: dt=0.100000, rms=0.704 (0.001%), neg=0, invalid=762 0069: dt=0.100000, rms=0.704 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.784, neg=0, invalid=762 0070: dt=5.771429, rms=0.761 (2.926%), neg=0, invalid=762 0071: dt=4.666667, rms=0.759 (0.285%), neg=0, invalid=762 0072: dt=1.008000, rms=0.759 (0.005%), neg=0, invalid=762 0073: dt=1.008000, rms=0.758 (0.003%), neg=0, invalid=762 0074: dt=1.008000, rms=0.759 (-0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.759, neg=0, invalid=762 0075: dt=0.000000, rms=0.759 (0.057%), neg=0, invalid=762 0076: dt=0.000000, rms=0.759 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.827, neg=0, invalid=762 0077: dt=0.448000, rms=0.825 (0.134%), neg=0, invalid=762 0078: dt=0.768000, rms=0.824 (0.121%), neg=0, invalid=762 0079: dt=0.768000, rms=0.823 (0.169%), neg=0, invalid=762 0080: dt=0.768000, rms=0.822 (0.132%), neg=0, invalid=762 0081: dt=0.768000, rms=0.822 (-0.096%), neg=0, invalid=762 0082: dt=1.792000, rms=0.820 (0.187%), neg=0, invalid=762 0083: dt=1.536000, rms=0.820 (0.039%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.821, neg=0, invalid=762 0084: dt=1.792000, rms=0.818 (0.275%), neg=0, invalid=762 0085: dt=0.096000, rms=0.818 (-0.001%), neg=0, invalid=762 0086: dt=0.096000, rms=0.818 (0.001%), neg=0, invalid=762 0087: dt=0.096000, rms=0.818 (-0.001%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.760, neg=0, invalid=762 0088: dt=0.953825, rms=0.736 (3.232%), neg=0, invalid=762 0089: dt=0.096000, rms=0.735 (0.159%), neg=0, invalid=762 0090: dt=0.096000, rms=0.735 (-0.115%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.735, neg=0, invalid=762 0091: dt=0.028000, rms=0.734 (0.084%), neg=0, invalid=762 0092: dt=0.016000, rms=0.734 (0.003%), neg=0, invalid=762 0093: dt=0.016000, rms=0.734 (-0.005%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.06770 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (988 voxels, overlap=0.119) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (988 voxels, peak = 10), gca=10.5 gca peak = 0.15565 (16) mri peak = 0.08798 (16) Right_Lateral_Ventricle (43): linear fit = 0.81 x + 0.0 (795 voxels, overlap=0.614) Right_Lateral_Ventricle (43): linear fit = 0.81 x + 0.0 (795 voxels, peak = 13), gca=13.0 gca peak = 0.26829 (96) mri peak = 0.05663 (91) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (1003 voxels, overlap=0.576) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (1003 voxels, peak = 90), gca=89.8 gca peak = 0.20183 (93) mri peak = 0.11111 (77) Left_Pallidum: unreasonable value (74.9/77.0), not in range [75, 135] - rejecting gca peak = 0.21683 (55) mri peak = 0.08174 (62) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (621 voxels, overlap=0.841) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (621 voxels, peak = 60), gca=60.2 gca peak = 0.30730 (58) mri peak = 0.06019 (65) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (589 voxels, overlap=0.893) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (589 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.05738 (101) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57291 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57291 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.04838 (104) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57324 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57324 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03925 (67) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (19919 voxels, overlap=0.905) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (19919 voxels, peak = 65), gca=64.6 gca peak = 0.15082 (58) mri peak = 0.03607 (61) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (17922 voxels, overlap=0.898) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (17922 voxels, peak = 62), gca=62.4 gca peak = 0.14161 (67) mri peak = 0.09925 (78) Right_Caudate (50): linear fit = 1.13 x + 0.0 (831 voxels, overlap=0.100) Right_Caudate (50): linear fit = 1.13 x + 0.0 (831 voxels, peak = 76), gca=76.0 gca peak = 0.15243 (71) mri peak = 0.08140 (71) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1033 voxels, overlap=0.960) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1033 voxels, peak = 70), gca=69.9 gca peak = 0.13336 (57) mri peak = 0.04497 (53) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (20891 voxels, overlap=0.970) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (20891 voxels, peak = 54), gca=53.9 gca peak = 0.13252 (56) mri peak = 0.03901 (54) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21984 voxels, overlap=0.996) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21984 voxels, peak = 54), gca=54.0 gca peak = 0.18181 (84) mri peak = 0.03150 (81) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (7659 voxels, overlap=0.874) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (7659 voxels, peak = 83), gca=82.7 gca peak = 0.20573 (83) mri peak = 0.04090 (82) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7627 voxels, overlap=0.960) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7627 voxels, peak = 83), gca=82.6 gca peak = 0.21969 (57) mri peak = 0.05170 (69) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (327 voxels, overlap=0.789) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (327 voxels, peak = 69), gca=69.3 gca peak = 0.39313 (56) mri peak = 0.08808 (60) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (288 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (288 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05563 (92) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5581 voxels, overlap=0.941) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5581 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.04955 (90) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4708 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4708 voxels, peak = 88), gca=87.6 gca peak = 0.13399 (79) mri peak = 0.03556 (90) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2402 voxels, overlap=0.828) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2402 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.06441 (73) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2438 voxels, overlap=0.896) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2438 voxels, peak = 77), gca=77.0 gca peak = 0.10025 (80) mri peak = 0.14509 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12111 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12111 voxels, peak = 84), gca=84.4 gca peak = 0.13281 (86) mri peak = 0.06515 (86) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1506 voxels, overlap=0.729) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1506 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.05971 (86) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1588 voxels, overlap=0.852) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1588 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.19056 (51) Third_Ventricle (14): linear fit = 2.17 x + 0.0 (82 voxels, overlap=0.026) Third_Ventricle (14): linear fit = 2.17 x + 0.0 (82 voxels, peak = 50), gca=50.0 gca peak = 0.15061 (21) mri peak = 0.13027 ( 6) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (240 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (240 voxels, peak = 6), gca=6.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Left_Pallidum = 0.20183 (93) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Left_Pallidum based on Right_Pallidum = 0.94 x + 0: 90 estimating mean gm scale to be 1.11 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.67 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.735, neg=0, invalid=762 0094: dt=110.976000, rms=0.728 (0.978%), neg=0, invalid=762 0095: dt=295.936000, rms=0.723 (0.668%), neg=0, invalid=762 0096: dt=129.472000, rms=0.721 (0.181%), neg=0, invalid=762 0097: dt=369.920000, rms=0.719 (0.359%), neg=0, invalid=762 0098: dt=73.984000, rms=0.718 (0.133%), neg=0, invalid=762 0099: dt=443.904000, rms=0.717 (0.102%), neg=0, invalid=762 0100: dt=129.472000, rms=0.716 (0.146%), neg=0, invalid=762 0101: dt=129.472000, rms=0.716 (0.033%), neg=0, invalid=762 0102: dt=129.472000, rms=0.716 (0.050%), neg=0, invalid=762 0103: dt=129.472000, rms=0.715 (0.078%), neg=0, invalid=762 0104: dt=129.472000, rms=0.714 (0.077%), neg=0, invalid=762 0105: dt=129.472000, rms=0.714 (0.076%), neg=0, invalid=762 0106: dt=129.472000, rms=0.713 (0.094%), neg=0, invalid=762 0107: dt=129.472000, rms=0.713 (0.084%), neg=0, invalid=762 0108: dt=129.472000, rms=0.712 (0.062%), neg=0, invalid=762 0109: dt=129.472000, rms=0.712 (0.043%), neg=0, invalid=762 0110: dt=129.472000, rms=0.712 (0.037%), neg=0, invalid=762 0111: dt=129.472000, rms=0.711 (0.033%), neg=0, invalid=762 0112: dt=129.472000, rms=0.711 (0.032%), neg=0, invalid=762 0113: dt=129.472000, rms=0.711 (0.048%), neg=0, invalid=762 0114: dt=129.472000, rms=0.710 (0.056%), neg=0, invalid=762 0115: dt=129.472000, rms=0.710 (0.053%), neg=0, invalid=762 0116: dt=129.472000, rms=0.710 (0.049%), neg=0, invalid=762 0117: dt=129.472000, rms=0.709 (0.047%), neg=0, invalid=762 0118: dt=129.472000, rms=0.709 (0.043%), neg=0, invalid=762 0119: dt=129.472000, rms=0.709 (0.043%), neg=0, invalid=762 0120: dt=129.472000, rms=0.708 (0.045%), neg=0, invalid=762 0121: dt=129.472000, rms=0.708 (0.049%), neg=0, invalid=762 0122: dt=129.472000, rms=0.708 (0.041%), neg=0, invalid=762 0123: dt=129.472000, rms=0.707 (0.045%), neg=0, invalid=762 0124: dt=129.472000, rms=0.707 (0.047%), neg=0, invalid=762 0125: dt=129.472000, rms=0.707 (0.048%), neg=0, invalid=762 0126: dt=129.472000, rms=0.706 (0.045%), neg=0, invalid=762 0127: dt=129.472000, rms=0.706 (0.042%), neg=0, invalid=762 0128: dt=129.472000, rms=0.706 (0.043%), neg=0, invalid=762 0129: dt=129.472000, rms=0.706 (0.046%), neg=0, invalid=762 0130: dt=129.472000, rms=0.705 (0.048%), neg=0, invalid=762 0131: dt=129.472000, rms=0.705 (0.048%), neg=0, invalid=762 0132: dt=129.472000, rms=0.705 (0.043%), neg=0, invalid=762 0133: dt=129.472000, rms=0.704 (0.040%), neg=0, invalid=762 0134: dt=129.472000, rms=0.704 (0.042%), neg=0, invalid=762 0135: dt=129.472000, rms=0.704 (0.044%), neg=0, invalid=762 0136: dt=129.472000, rms=0.703 (0.034%), neg=0, invalid=762 0137: dt=129.472000, rms=0.703 (0.034%), neg=0, invalid=762 0138: dt=129.472000, rms=0.703 (0.030%), neg=0, invalid=762 0139: dt=129.472000, rms=0.703 (0.027%), neg=0, invalid=762 0140: dt=129.472000, rms=0.703 (0.034%), neg=0, invalid=762 0141: dt=129.472000, rms=0.702 (0.030%), neg=0, invalid=762 0142: dt=129.472000, rms=0.702 (0.025%), neg=0, invalid=762 0143: dt=129.472000, rms=0.702 (0.020%), neg=0, invalid=762 0144: dt=517.888000, rms=0.702 (0.003%), neg=0, invalid=762 0145: dt=517.888000, rms=0.702 (0.008%), neg=0, invalid=762 0146: dt=517.888000, rms=0.702 (-0.314%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.702, neg=0, invalid=762 0147: dt=129.472000, rms=0.701 (0.254%), neg=0, invalid=762 0148: dt=369.920000, rms=0.700 (0.123%), neg=0, invalid=762 0149: dt=129.472000, rms=0.699 (0.081%), neg=0, invalid=762 0150: dt=517.888000, rms=0.698 (0.093%), neg=0, invalid=762 0151: dt=129.472000, rms=0.698 (0.056%), neg=0, invalid=762 0152: dt=221.952000, rms=0.698 (0.026%), neg=0, invalid=762 0153: dt=221.952000, rms=0.698 (0.039%), neg=0, invalid=762 0154: dt=221.952000, rms=0.697 (0.067%), neg=0, invalid=762 0155: dt=221.952000, rms=0.697 (0.049%), neg=0, invalid=762 0156: dt=221.952000, rms=0.696 (0.081%), neg=0, invalid=762 0157: dt=221.952000, rms=0.696 (0.058%), neg=0, invalid=762 0158: dt=221.952000, rms=0.695 (0.059%), neg=0, invalid=762 0159: dt=221.952000, rms=0.695 (0.051%), neg=0, invalid=762 0160: dt=221.952000, rms=0.695 (0.051%), neg=0, invalid=762 0161: dt=221.952000, rms=0.694 (0.055%), neg=0, invalid=762 0162: dt=221.952000, rms=0.694 (0.030%), neg=0, invalid=762 0163: dt=221.952000, rms=0.694 (0.049%), neg=0, invalid=762 0164: dt=221.952000, rms=0.694 (0.036%), neg=0, invalid=762 0165: dt=221.952000, rms=0.693 (0.024%), neg=0, invalid=762 0166: dt=221.952000, rms=0.693 (0.047%), neg=0, invalid=762 0167: dt=221.952000, rms=0.693 (0.036%), neg=0, invalid=762 0168: dt=221.952000, rms=0.693 (0.023%), neg=0, invalid=762 0169: dt=221.952000, rms=0.692 (0.027%), neg=0, invalid=762 0170: dt=221.952000, rms=0.692 (0.037%), neg=0, invalid=762 0171: dt=221.952000, rms=0.692 (0.025%), neg=0, invalid=762 0172: dt=221.952000, rms=0.692 (0.011%), neg=0, invalid=762 0173: dt=221.952000, rms=0.692 (0.050%), neg=0, invalid=762 0174: dt=221.952000, rms=0.691 (0.037%), neg=0, invalid=762 0175: dt=221.952000, rms=0.691 (0.016%), neg=0, invalid=762 0176: dt=221.952000, rms=0.691 (0.025%), neg=0, invalid=762 0177: dt=221.952000, rms=0.691 (0.020%), neg=0, invalid=762 0178: dt=32.368000, rms=0.691 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.692, neg=0, invalid=762 0179: dt=36.288000, rms=0.691 (0.229%), neg=0, invalid=762 0180: dt=103.680000, rms=0.689 (0.181%), neg=0, invalid=762 0181: dt=331.776000, rms=0.682 (1.141%), neg=0, invalid=762 0182: dt=55.652174, rms=0.680 (0.260%), neg=0, invalid=762 0183: dt=414.720000, rms=0.674 (0.821%), neg=0, invalid=762 0184: dt=36.288000, rms=0.671 (0.517%), neg=0, invalid=762 0185: dt=36.288000, rms=0.670 (0.141%), neg=0, invalid=762 0186: dt=331.776000, rms=0.668 (0.291%), neg=0, invalid=762 0187: dt=62.208000, rms=0.666 (0.318%), neg=0, invalid=762 0188: dt=82.944000, rms=0.665 (0.100%), neg=0, invalid=762 0189: dt=82.944000, rms=0.664 (0.141%), neg=0, invalid=762 0190: dt=36.288000, rms=0.664 (0.090%), neg=0, invalid=762 0191: dt=580.608000, rms=0.659 (0.653%), neg=0, invalid=762 0192: dt=36.288000, rms=0.659 (0.082%), neg=0, invalid=762 0193: dt=580.608000, rms=0.656 (0.437%), neg=0, invalid=762 0194: dt=64.000000, rms=0.655 (0.100%), neg=0, invalid=762 0195: dt=124.416000, rms=0.655 (0.083%), neg=0, invalid=762 0196: dt=62.208000, rms=0.654 (0.075%), neg=0, invalid=762 0197: dt=103.680000, rms=0.654 (0.057%), neg=0, invalid=762 0198: dt=36.288000, rms=0.653 (0.051%), neg=0, invalid=762 0199: dt=580.608000, rms=0.651 (0.359%), neg=0, invalid=762 0200: dt=36.288000, rms=0.651 (0.041%), neg=0, invalid=762 0201: dt=36.288000, rms=0.651 (0.024%), neg=0, invalid=762 0202: dt=36.288000, rms=0.650 (0.038%), neg=0, invalid=762 0203: dt=36.288000, rms=0.650 (0.051%), neg=0, invalid=762 0204: dt=36.288000, rms=0.650 (0.023%), neg=0, invalid=762 0205: dt=36.288000, rms=0.650 (0.039%), neg=0, invalid=762 0206: dt=18.144000, rms=0.650 (0.010%), neg=0, invalid=762 0207: dt=2.268000, rms=0.650 (0.001%), neg=0, invalid=762 0208: dt=1.944000, rms=0.650 (0.001%), neg=0, invalid=762 0209: dt=0.060750, rms=0.650 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.650, neg=0, invalid=762 0210: dt=0.141750, rms=0.650 (0.097%), neg=0, invalid=762 0211: dt=0.141750, rms=0.650 (0.002%), neg=0, invalid=762 0212: dt=0.070875, rms=0.650 (0.001%), neg=0, invalid=762 0213: dt=0.017719, rms=0.650 (0.000%), neg=0, invalid=762 0214: dt=0.008859, rms=0.650 (0.000%), neg=0, invalid=762 0215: dt=0.005670, rms=0.650 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.657, neg=0, invalid=762 0216: dt=32.000000, rms=0.646 (1.645%), neg=0, invalid=762 0217: dt=2.000000, rms=0.645 (0.077%), neg=0, invalid=762 0218: dt=0.037500, rms=0.645 (0.002%), neg=0, invalid=762 0219: dt=0.002344, rms=0.645 (0.000%), neg=0, invalid=762 0220: dt=0.000146, rms=0.645 (0.000%), neg=0, invalid=762 0221: dt=0.000073, rms=0.645 (0.000%), neg=0, invalid=762 0222: dt=0.000000, rms=0.645 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0223: dt=44.800000, rms=0.634 (1.852%), neg=0, invalid=762 0224: dt=2.800000, rms=0.633 (0.111%), neg=0, invalid=762 0225: dt=2.800000, rms=0.633 (0.099%), neg=0, invalid=762 0226: dt=2.000000, rms=0.632 (0.063%), neg=0, invalid=762 0227: dt=0.175000, rms=0.632 (0.007%), neg=0, invalid=762 0228: dt=0.175000, rms=0.632 (0.006%), neg=0, invalid=762 0229: dt=0.021875, rms=0.632 (0.001%), neg=0, invalid=762 0230: dt=0.010937, rms=0.632 (0.000%), neg=0, invalid=762 0231: dt=0.002734, rms=0.632 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0232: dt=0.000984, rms=0.651 (0.082%), neg=0, invalid=762 0233: dt=0.000984, rms=0.651 (0.000%), neg=0, invalid=762 0234: dt=0.000123, rms=0.651 (0.000%), neg=0, invalid=762 0235: dt=0.000062, rms=0.651 (0.000%), neg=0, invalid=762 0236: dt=0.000015, rms=0.651 (0.000%), neg=0, invalid=762 0237: dt=0.000000, rms=0.651 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0238: dt=25.558101, rms=0.627 (3.656%), neg=0, invalid=762 0239: dt=14.790582, rms=0.617 (1.579%), neg=0, invalid=762 0240: dt=10.249275, rms=0.615 (0.385%), neg=0, invalid=762 0241: dt=30.800000, rms=0.611 (0.676%), neg=0, invalid=762 0242: dt=7.152542, rms=0.609 (0.336%), neg=0, invalid=762 0243: dt=16.128000, rms=0.608 (0.200%), neg=0, invalid=762 0244: dt=21.224490, rms=0.606 (0.208%), neg=0, invalid=762 0245: dt=10.589928, rms=0.605 (0.156%), neg=0, invalid=762 0246: dt=17.739130, rms=0.605 (0.148%), neg=0, invalid=762 0247: dt=9.345133, rms=0.604 (0.108%), neg=0, invalid=762 0248: dt=17.684211, rms=0.603 (0.117%), neg=0, invalid=762 0249: dt=8.677966, rms=0.603 (0.086%), neg=0, invalid=762 0250: dt=16.421053, rms=0.602 (0.107%), neg=0, invalid=762 0251: dt=8.200000, rms=0.602 (0.067%), neg=0, invalid=762 0252: dt=18.285714, rms=0.601 (0.100%), neg=0, invalid=762 0253: dt=7.589744, rms=0.601 (0.064%), neg=0, invalid=762 0254: dt=22.222222, rms=0.600 (0.087%), neg=0, invalid=762 0255: dt=7.917526, rms=0.600 (0.062%), neg=0, invalid=762 0256: dt=16.128000, rms=0.599 (0.074%), neg=0, invalid=762 0257: dt=7.641791, rms=0.599 (0.049%), neg=0, invalid=762 0258: dt=7.641791, rms=0.599 (0.042%), neg=0, invalid=762 0259: dt=7.641791, rms=0.598 (0.063%), neg=0, invalid=762 0260: dt=7.641791, rms=0.598 (0.096%), neg=0, invalid=762 0261: dt=7.641791, rms=0.597 (0.110%), neg=0, invalid=762 0262: dt=7.641791, rms=0.596 (0.149%), neg=0, invalid=762 0263: dt=7.641791, rms=0.595 (0.157%), neg=0, invalid=762 0264: dt=7.641791, rms=0.594 (0.139%), neg=0, invalid=762 0265: dt=7.641791, rms=0.594 (0.125%), neg=0, invalid=762 0266: dt=7.641791, rms=0.593 (0.129%), neg=0, invalid=762 0267: dt=7.641791, rms=0.592 (0.113%), neg=0, invalid=762 0268: dt=7.641791, rms=0.592 (0.106%), neg=0, invalid=762 0269: dt=7.641791, rms=0.591 (0.097%), neg=0, invalid=762 0270: dt=7.641791, rms=0.591 (0.096%), neg=0, invalid=762 0271: dt=7.641791, rms=0.590 (0.078%), neg=0, invalid=762 0272: dt=7.641791, rms=0.590 (0.080%), neg=0, invalid=762 0273: dt=7.641791, rms=0.589 (0.078%), neg=0, invalid=762 0274: dt=7.641791, rms=0.589 (0.078%), neg=0, invalid=762 0275: dt=7.641791, rms=0.588 (0.070%), neg=0, invalid=762 0276: dt=7.641791, rms=0.588 (0.059%), neg=0, invalid=762 0277: dt=7.641791, rms=0.588 (0.049%), neg=0, invalid=762 0278: dt=7.641791, rms=0.587 (0.038%), neg=0, invalid=762 0279: dt=7.641791, rms=0.587 (0.043%), neg=0, invalid=762 0280: dt=7.641791, rms=0.587 (0.043%), neg=0, invalid=762 0281: dt=7.641791, rms=0.587 (0.037%), neg=0, invalid=762 0282: dt=7.641791, rms=0.586 (0.036%), neg=0, invalid=762 0283: dt=7.641791, rms=0.586 (0.039%), neg=0, invalid=762 0284: dt=7.641791, rms=0.586 (0.031%), neg=0, invalid=762 0285: dt=7.641791, rms=0.586 (0.026%), neg=0, invalid=762 0286: dt=7.641791, rms=0.586 (0.036%), neg=0, invalid=762 0287: dt=7.641791, rms=0.586 (0.028%), neg=0, invalid=762 0288: dt=7.641791, rms=0.585 (0.026%), neg=0, invalid=762 0289: dt=7.641791, rms=0.585 (0.020%), neg=0, invalid=762 0290: dt=7.641791, rms=0.585 (0.029%), neg=0, invalid=762 0291: dt=7.641791, rms=0.585 (0.022%), neg=0, invalid=762 0292: dt=7.641791, rms=0.585 (0.020%), neg=0, invalid=762 0293: dt=6.912000, rms=0.585 (0.009%), neg=0, invalid=762 0294: dt=6.912000, rms=0.585 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0295: dt=0.000000, rms=0.601 (0.082%), neg=0, invalid=762 0296: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762 0297: dt=0.100000, rms=0.601 (-0.173%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0298: dt=0.000000, rms=0.601 (0.082%), neg=0, invalid=762 0299: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762 0300: dt=0.100000, rms=0.601 (-0.156%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.574, neg=0, invalid=762 0301: dt=0.448000, rms=0.557 (3.029%), neg=0, invalid=762 0302: dt=0.448000, rms=0.553 (0.663%), neg=0, invalid=762 0303: dt=0.448000, rms=0.551 (0.387%), neg=0, invalid=762 0304: dt=0.448000, rms=0.550 (0.194%), neg=0, invalid=762 0305: dt=0.500000, rms=0.549 (0.197%), neg=0, invalid=762 0306: dt=0.448000, rms=0.549 (0.083%), neg=0, invalid=762 0307: dt=0.448000, rms=0.548 (0.112%), neg=0, invalid=762 0308: dt=0.448000, rms=0.548 (0.042%), neg=0, invalid=762 0309: dt=0.448000, rms=0.547 (0.079%), neg=0, invalid=762 0310: dt=0.448000, rms=0.547 (0.087%), neg=0, invalid=762 0311: dt=0.448000, rms=0.546 (0.088%), neg=0, invalid=762 0312: dt=0.448000, rms=0.546 (0.107%), neg=0, invalid=762 0313: dt=0.448000, rms=0.546 (0.015%), neg=0, invalid=762 0314: dt=0.448000, rms=0.546 (-0.005%), neg=0, invalid=762 0315: dt=0.028000, rms=0.546 (0.000%), neg=0, invalid=762 0316: dt=0.028000, rms=0.546 (0.001%), neg=0, invalid=762 0317: dt=0.096000, rms=0.546 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0318: dt=0.448000, rms=0.537 (1.596%), neg=0, invalid=762 0319: dt=0.448000, rms=0.536 (0.239%), neg=0, invalid=762 0320: dt=0.448000, rms=0.536 (0.070%), neg=0, invalid=762 0321: dt=0.448000, rms=0.536 (0.041%), neg=0, invalid=762 0322: dt=0.448000, rms=0.536 (-0.006%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0323: dt=0.000000, rms=0.533 (0.108%), neg=0, invalid=762 0324: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0325: dt=8.092000, rms=0.533 (0.109%), neg=0, invalid=762 0326: dt=8.092000, rms=0.533 (0.003%), neg=0, invalid=762 0327: dt=8.092000, rms=0.533 (0.001%), neg=0, invalid=762 0328: dt=8.092000, rms=0.533 (0.000%), neg=0, invalid=762 0329: dt=8.092000, rms=0.533 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0330: dt=2.268000, rms=0.533 (0.112%), neg=0, invalid=762 0331: dt=2.268000, rms=0.533 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0332: dt=89.342282, rms=0.532 (0.360%), neg=0, invalid=762 0333: dt=62.208000, rms=0.531 (0.112%), neg=0, invalid=762 0334: dt=62.208000, rms=0.531 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0335: dt=11.200000, rms=0.530 (0.396%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0336: dt=11.200000, rms=0.529 (0.121%), neg=0, invalid=762 0337: dt=11.200000, rms=0.529 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0338: dt=11.200000, rms=0.529 (-0.062%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0339: dt=38.400000, rms=0.522 (1.295%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0340: dt=19.912525, rms=0.520 (0.376%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0341: dt=38.400000, rms=0.519 (0.298%), neg=0, invalid=762 0342: dt=11.200000, rms=0.518 (0.172%), neg=0, invalid=762 0343: dt=11.200000, rms=0.517 (0.104%), neg=0, invalid=762 0344: dt=11.200000, rms=0.517 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0345: dt=11.200000, rms=0.516 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0346: dt=11.200000, rms=0.515 (0.223%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0347: dt=11.200000, rms=0.514 (0.225%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0348: dt=11.200000, rms=0.512 (0.234%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0349: dt=11.200000, rms=0.511 (0.217%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0350: dt=11.200000, rms=0.510 (0.189%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0351: dt=11.200000, rms=0.509 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0352: dt=11.200000, rms=0.508 (0.176%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0353: dt=11.200000, rms=0.508 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0354: dt=11.200000, rms=0.507 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0355: dt=11.200000, rms=0.506 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0356: dt=11.200000, rms=0.505 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0357: dt=11.200000, rms=0.505 (0.102%), neg=0, invalid=762 0358: dt=11.200000, rms=0.505 (0.012%), neg=0, invalid=762 0359: dt=11.200000, rms=0.505 (0.008%), neg=0, invalid=762 0360: dt=11.200000, rms=0.505 (0.008%), neg=0, invalid=762 0361: dt=11.200000, rms=0.505 (0.016%), neg=0, invalid=762 0362: dt=11.200000, rms=0.505 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0363: dt=2.304000, rms=0.509 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0364: dt=0.864000, rms=0.509 (0.005%), neg=0, invalid=762 0365: dt=0.864000, rms=0.509 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0366: dt=6.933333, rms=0.508 (0.247%), neg=0, invalid=762 0367: dt=10.850575, rms=0.508 (0.114%), neg=0, invalid=762 0368: dt=10.850575, rms=0.507 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0369: dt=10.850575, rms=0.506 (0.282%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0370: dt=10.850575, rms=0.504 (0.358%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0371: dt=10.850575, rms=0.501 (0.482%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0372: dt=10.850575, rms=0.498 (0.586%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0373: dt=10.850575, rms=0.496 (0.551%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0374: dt=10.850575, rms=0.494 (0.351%), neg=0, invalid=762 0375: dt=10.850575, rms=0.493 (0.098%), neg=0, invalid=762 0376: dt=10.850575, rms=0.493 (-0.052%), neg=0, invalid=762 0377: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.501, neg=0, invalid=762 0378: dt=0.000000, rms=0.500 (0.138%), neg=0, invalid=762 0379: dt=0.000000, rms=0.500 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.501, neg=0, invalid=762 0380: dt=0.000000, rms=0.500 (0.138%), neg=0, invalid=762 0381: dt=0.000000, rms=0.500 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 iter 0, gcam->neg = 1171 after 11 iterations, nbhd size=1, neg = 0 0382: dt=1.601331, rms=0.466 (4.780%), neg=0, invalid=762 0383: dt=0.000013, rms=0.466 (0.011%), neg=0, invalid=762 0384: dt=0.000013, rms=0.466 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0385: dt=0.096000, rms=0.466 (0.210%), neg=0, invalid=762 0386: dt=0.007000, rms=0.466 (0.000%), neg=0, invalid=762 0387: dt=0.007000, rms=0.466 (0.000%), neg=0, invalid=762 0388: dt=0.007000, rms=0.466 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0389: dt=0.000000, rms=0.457 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0390: dt=2.023000, rms=0.457 (0.000%), neg=0, invalid=762 0391: dt=0.289000, rms=0.457 (0.000%), neg=0, invalid=762 0392: dt=0.289000, rms=0.457 (0.000%), neg=0, invalid=762 0393: dt=0.289000, rms=0.457 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0394: dt=0.000000, rms=0.457 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0395: dt=9.072000, rms=0.457 (0.007%), neg=0, invalid=762 0396: dt=9.072000, rms=0.457 (0.003%), neg=0, invalid=762 0397: dt=9.072000, rms=0.457 (0.001%), neg=0, invalid=762 0398: dt=9.072000, rms=0.457 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 0399: dt=2.800000, rms=0.457 (0.022%), neg=0, invalid=762 0400: dt=1.200000, rms=0.457 (0.002%), neg=0, invalid=762 0401: dt=1.200000, rms=0.457 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0402: dt=44.800000, rms=0.455 (0.411%), neg=0, invalid=762 0403: dt=32.000000, rms=0.454 (0.160%), neg=0, invalid=762 0404: dt=32.000000, rms=0.454 (0.113%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0405: dt=32.000000, rms=0.453 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0406: dt=32.000000, rms=0.453 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 8 iterations, nbhd size=1, neg = 0 0407: dt=32.000000, rms=0.452 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0408: dt=32.000000, rms=0.451 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 10 iterations, nbhd size=1, neg = 0 0409: dt=32.000000, rms=0.451 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0410: dt=32.000000, rms=0.450 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0411: dt=32.000000, rms=0.450 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0412: dt=32.000000, rms=0.450 (0.082%), neg=0, invalid=762 0413: dt=25.600000, rms=0.449 (0.046%), neg=0, invalid=762 0414: dt=25.600000, rms=0.449 (0.023%), neg=0, invalid=762 0415: dt=25.600000, rms=0.449 (0.027%), neg=0, invalid=762 0416: dt=25.600000, rms=0.449 (0.038%), neg=0, invalid=762 0417: dt=25.600000, rms=0.449 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0418: dt=25.600000, rms=0.449 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0419: dt=25.600000, rms=0.449 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0420: dt=0.216000, rms=0.452 (0.000%), neg=0, invalid=762 0421: dt=0.000703, rms=0.452 (0.000%), neg=0, invalid=762 0422: dt=0.000703, rms=0.452 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0423: dt=10.084034, rms=0.451 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0424: dt=25.379310, rms=0.450 (0.248%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0425: dt=24.242424, rms=0.449 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 0426: dt=24.242424, rms=0.449 (-0.498%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0427: dt=0.000050, rms=0.454 (0.000%), neg=0, invalid=762 0428: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0429: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.446, neg=0, invalid=762 iter 0, gcam->neg = 372 after 12 iterations, nbhd size=1, neg = 0 0430: dt=1.083179, rms=0.438 (1.716%), neg=0, invalid=762 0431: dt=0.000023, rms=0.438 (0.000%), neg=0, invalid=762 0432: dt=0.000023, rms=0.438 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0433: dt=0.320000, rms=0.437 (0.352%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0434: dt=0.583333, rms=0.434 (0.592%), neg=0, invalid=762 0435: dt=0.384000, rms=0.433 (0.168%), neg=0, invalid=762 0436: dt=0.384000, rms=0.432 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0437: dt=0.384000, rms=0.432 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 1 iterations, nbhd size=0, neg = 0 0438: dt=0.384000, rms=0.432 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 8 iterations, nbhd size=1, neg = 0 0439: dt=0.384000, rms=0.432 (-0.030%), neg=0, invalid=762 0440: dt=0.256000, rms=0.431 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0441: dt=0.320000, rms=0.431 (0.030%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 19 minutes and 49 seconds. mri_ca_register utimesec 8385.839158 mri_ca_register stimesec 7.525855 mri_ca_register ru_maxrss 1339828 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4245432 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 64912 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 1256 mri_ca_register ru_nivcsw 20167 FSRUNTIME@ mri_ca_register 2.3303 hours 1 threads #-------------------------------------- #@# SubCort Seg Fri Oct 27 00:20:12 CEST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname tars-623 machine x86_64 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.98 Atlas used for the 3D morph was /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.08194 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (262 voxels, overlap=0.401) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (262 voxels, peak = 9), gca=8.9 gca peak = 0.17677 (13) mri peak = 0.10423 (10) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (355 voxels, overlap=0.558) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (355 voxels, peak = 9), gca=9.0 gca peak = 0.28129 (95) mri peak = 0.06825 (99) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (672 voxels, overlap=1.021) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (672 voxels, peak = 92), gca=91.7 gca peak = 0.16930 (96) mri peak = 0.12789 (92) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (563 voxels, overlap=0.974) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (563 voxels, peak = 93), gca=92.6 gca peak = 0.24553 (55) mri peak = 0.07523 (62) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (572 voxels, overlap=1.013) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (572 voxels, peak = 60), gca=60.2 gca peak = 0.30264 (59) mri peak = 0.06387 (58) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (570 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (570 voxels, peak = 60), gca=60.5 gca peak = 0.07580 (103) mri peak = 0.05593 (101) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (41078 voxels, overlap=0.784) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (41078 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.04577 (104) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43488 voxels, overlap=0.794) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43488 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.03751 (62) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28727 voxels, overlap=0.967) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (28727 voxels, peak = 61), gca=60.6 gca peak = 0.11620 (58) mri peak = 0.03770 (61) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (24768 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (24768 voxels, peak = 62), gca=62.4 gca peak = 0.30970 (66) mri peak = 0.09189 (78) Right_Caudate (50): linear fit = 1.14 x + 0.0 (880 voxels, overlap=0.241) Right_Caudate (50): linear fit = 1.14 x + 0.0 (880 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.08921 (76) Left_Caudate (11): linear fit = 0.98 x + 0.0 (825 voxels, overlap=1.003) Left_Caudate (11): linear fit = 0.98 x + 0.0 (825 voxels, peak = 67), gca=67.3 gca peak = 0.13902 (56) mri peak = 0.04979 (51) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22467 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22467 voxels, peak = 53), gca=52.9 gca peak = 0.14777 (55) mri peak = 0.04159 (55) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21138 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (21138 voxels, peak = 53), gca=53.1 gca peak = 0.16765 (84) mri peak = 0.05843 (83) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5964 voxels, overlap=0.986) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5964 voxels, peak = 83), gca=82.7 gca peak = 0.18739 (84) mri peak = 0.05754 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5089 voxels, overlap=0.911) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5089 voxels, peak = 86), gca=86.1 gca peak = 0.29869 (57) mri peak = 0.07292 (60) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (296 voxels, overlap=1.044) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (296 voxels, peak = 58), gca=57.9 gca peak = 0.33601 (57) mri peak = 0.06015 (60) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (283 voxels, overlap=1.040) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (283 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.05948 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4428 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4428 voxels, peak = 90), gca=89.6 gca peak = 0.11793 (83) mri peak = 0.05718 (88) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4026 voxels, overlap=0.980) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4026 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.06573 (74) Left_Putamen (12): linear fit = 0.95 x + 0.0 (3134 voxels, overlap=0.715) Left_Putamen (12): linear fit = 0.95 x + 0.0 (3134 voxels, peak = 77), gca=77.4 gca peak = 0.10360 (77) mri peak = 0.07534 (75) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2232 voxels, overlap=0.820) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2232 voxels, peak = 74), gca=73.5 gca peak = 0.08424 (78) mri peak = 0.15709 (80) Brain_Stem: unreasonable value (79.2/80.0), not in range [80, 110] - rejecting gca peak = 0.12631 (89) mri peak = 0.06160 (94) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1034 voxels, overlap=0.830) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1034 voxels, peak = 94), gca=93.9 gca peak = 0.14500 (87) mri peak = 0.06257 (84) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1203 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1203 voxels, peak = 85), gca=84.8 gca peak = 0.14975 (24) mri peak = 0.14488 (51) gca peak = 0.19357 (14) mri peak = 0.14913 ( 3) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (115 voxels, overlap=0.016) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (115 voxels, peak = 2), gca=1.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.05 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.57 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.29497 ( 9) mri peak = 0.08194 ( 8) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (262 voxels, overlap=0.994) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (262 voxels, peak = 9), gca=9.5 gca peak = 0.27800 ( 9) mri peak = 0.10423 (10) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (355 voxels, overlap=0.928) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (355 voxels, peak = 9), gca=9.5 gca peak = 0.25179 (91) mri peak = 0.06825 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (672 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (672 voxels, peak = 91), gca=90.5 gca peak = 0.18582 (93) mri peak = 0.12789 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (563 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (563 voxels, peak = 93), gca=92.5 gca peak = 0.25839 (61) mri peak = 0.07523 (62) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (572 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (572 voxels, peak = 61), gca=61.0 gca peak = 0.28192 (58) mri peak = 0.06387 (58) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (570 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (570 voxels, peak = 58), gca=58.0 gca peak = 0.07614 (105) mri peak = 0.05593 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41078 voxels, overlap=0.864) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41078 voxels, peak = 104), gca=104.5 gca peak = 0.07799 (109) mri peak = 0.04577 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43488 voxels, overlap=0.916) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43488 voxels, peak = 109), gca=109.0 gca peak = 0.09240 (60) mri peak = 0.03751 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28727 voxels, overlap=0.983) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28727 voxels, peak = 62), gca=61.5 gca peak = 0.11117 (62) mri peak = 0.03770 (61) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24768 voxels, overlap=0.973) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (24768 voxels, peak = 64), gca=63.5 gca peak = 0.24573 (76) mri peak = 0.09189 (78) Right_Caudate (50): linear fit = 1.01 x + 0.0 (880 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.01 x + 0.0 (880 voxels, peak = 77), gca=77.1 gca peak = 0.13720 (67) mri peak = 0.08921 (76) Left_Caudate (11): linear fit = 1.00 x + 0.0 (825 voxels, overlap=1.001) Left_Caudate (11): linear fit = 1.00 x + 0.0 (825 voxels, peak = 67), gca=67.0 gca peak = 0.14851 (53) mri peak = 0.04979 (51) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (22467 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (22467 voxels, peak = 53), gca=53.0 gca peak = 0.15535 (53) mri peak = 0.04159 (55) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21138 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21138 voxels, peak = 53), gca=53.0 gca peak = 0.16203 (83) mri peak = 0.05843 (83) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5964 voxels, overlap=0.977) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5964 voxels, peak = 83), gca=82.6 gca peak = 0.16001 (86) mri peak = 0.05754 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5089 voxels, overlap=0.966) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5089 voxels, peak = 86), gca=85.6 gca peak = 0.30225 (59) mri peak = 0.07292 (60) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (296 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (296 voxels, peak = 60), gca=60.5 gca peak = 0.33137 (60) mri peak = 0.06015 (60) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (283 voxels, overlap=1.039) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (283 voxels, peak = 62), gca=61.5 gca peak = 0.10237 (89) mri peak = 0.05948 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4428 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4428 voxels, peak = 90), gca=90.3 gca peak = 0.09701 (90) mri peak = 0.05718 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4026 voxels, overlap=1.000) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4026 voxels, peak = 90), gca=89.6 gca peak = 0.08002 (79) mri peak = 0.06573 (74) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3134 voxels, overlap=0.887) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3134 voxels, peak = 79), gca=78.6 gca peak = 0.11291 (72) mri peak = 0.07534 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2232 voxels, overlap=0.935) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2232 voxels, peak = 72), gca=71.6 gca peak = 0.08598 (81) mri peak = 0.15709 (80) Brain_Stem: unreasonable value (79.8/80.0), not in range [80, 110] - rejecting gca peak = 0.13330 (94) mri peak = 0.06160 (94) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1034 voxels, overlap=0.884) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1034 voxels, peak = 93), gca=92.6 gca peak = 0.14445 (85) mri peak = 0.06257 (84) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1203 voxels, overlap=0.878) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1203 voxels, peak = 91), gca=90.5 gca peak = 0.29549 (15) mri peak = 0.14488 (51) gca peak = 0.29582 ( 8) mri peak = 0.14913 ( 3) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (115 voxels, overlap=0.559) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (115 voxels, peak = 2), gca=1.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15047 (33) gca peak Left_Thalamus = 1.00000 (99) gca peak Third_Ventricle = 0.29549 (15) gca peak Fourth_Ventricle = 0.29582 ( 8) gca peak Brain_Stem = 0.08598 (81) gca peak CSF = 0.26369 (21) gca peak Left_Accumbens_area = 0.51250 (60) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.20543 (25) gca peak Right_Accumbens_area = 0.29775 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.89470 (18) gca peak WM_hypointensities = 0.07030 (78) gca peak non_WM_hypointensities = 0.08309 (45) gca peak Optic_Chiasm = 0.71088 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.05 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 95733 voxels changed in iteration 0 of unlikely voxel relabeling 331 voxels changed in iteration 1 of unlikely voxel relabeling 71 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 51554 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 397 hippocampal voxels changed. 4 amygdala voxels changed. pass 1: 86021 changed. image ll: -2.176, PF=0.500 pass 2: 26135 changed. image ll: -2.176, PF=0.500 pass 3: 8497 changed. pass 4: 3154 changed. 65461 voxels changed in iteration 0 of unlikely voxel relabeling 255 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 9624 voxels changed in iteration 0 of unlikely voxel relabeling 83 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8292 voxels changed in iteration 0 of unlikely voxel relabeling 86 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6243 voxels changed in iteration 0 of unlikely voxel relabeling 33 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3746.111504 mri_ca_label stimesec 1.476775 mri_ca_label ru_maxrss 2116740 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 741966 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 64904 mri_ca_label ru_oublock 480 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 191 mri_ca_label ru_nivcsw 9142 auto-labeling took 62 minutes and 26 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/cc_up.lta 0050418 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/norm.mgz 55249 voxels in left wm, 53910 in right wm, xrange [115, 127] searching rotation angles z=[-3 11], y=[-5 9] searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.7 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.7 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.5 searching scale 1 Z rot 10.7 global minimum found at slice 120.4, rotations (1.82, 4.00) final transformation (x=120.4, yr=1.820, zr=3.997): 0.99706 -0.06970 0.03168 11.18684; 0.06967 0.99757 0.00221 23.60376; -0.03175 -0.00000 0.99950 21.87768; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 96 110 eigenvectors: 0.00339 -0.01445 0.99989; -0.02829 -0.99950 -0.01435; 0.99959 -0.02824 -0.00380; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.auto.mgz... corpus callosum segmentation took 1.1 minutes #-------------------------------------- #@# Merge ASeg Fri Oct 27 01:23:45 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Oct 27 01:23:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1350 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 99 gm peak at 63 (63), valley at 12 (12) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 88 (88), valley at 85 (85) csf peak at 60, setting threshold to 78 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 15 seconds. #-------------------------------------------- #@# Mask BFS Fri Oct 27 01:27:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1512859 voxels in mask (pct= 9.02) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Oct 27 01:27:02 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.6 +- 6.2 [79.0 --> 125.0] GM (69.0) : 67.0 +- 10.8 [30.0 --> 95.0] setting bottom of white matter range to 77.9 setting top of gray matter range to 88.7 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... 10533 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4342 filled 3770 bright non-wm voxels segmented. 4336 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.52 minutes reading wm segmentation from wm.seg.mgz... 438 voxels added to wm to prevent paths from MTL structures to cortex 4776 additional wm voxels added 0 additional wm voxels added SEG EDIT: 46314 voxels turned on, 16547 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 87 new 87 115,126,128 old 87 new 87 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.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-): 47 found - 47 modified | TOTAL: 81 pass 2 (xy-): 0 found - 47 modified | TOTAL: 81 pass 1 (yz+): 42 found - 42 modified | TOTAL: 123 pass 2 (yz+): 0 found - 42 modified | TOTAL: 123 pass 1 (yz-): 45 found - 45 modified | TOTAL: 168 pass 2 (yz-): 0 found - 45 modified | TOTAL: 168 pass 1 (xz+): 39 found - 39 modified | TOTAL: 207 pass 2 (xz+): 0 found - 39 modified | TOTAL: 207 pass 1 (xz-): 35 found - 35 modified | TOTAL: 242 pass 2 (xz-): 0 found - 35 modified | TOTAL: 242 Iteration Number : 1 pass 1 (+++): 34 found - 34 modified | TOTAL: 34 pass 2 (+++): 0 found - 34 modified | TOTAL: 34 pass 1 (+++): 56 found - 56 modified | TOTAL: 90 pass 2 (+++): 0 found - 56 modified | TOTAL: 90 pass 1 (+++): 48 found - 48 modified | TOTAL: 138 pass 2 (+++): 0 found - 48 modified | TOTAL: 138 pass 1 (+++): 65 found - 65 modified | TOTAL: 203 pass 2 (+++): 0 found - 65 modified | TOTAL: 203 Iteration Number : 1 pass 1 (++): 189 found - 189 modified | TOTAL: 189 pass 2 (++): 0 found - 189 modified | TOTAL: 189 pass 1 (+-): 192 found - 192 modified | TOTAL: 381 pass 2 (+-): 0 found - 192 modified | TOTAL: 381 pass 1 (--): 146 found - 146 modified | TOTAL: 527 pass 2 (--): 1 found - 147 modified | TOTAL: 528 pass 3 (--): 0 found - 147 modified | TOTAL: 528 pass 1 (-+): 170 found - 170 modified | TOTAL: 698 pass 2 (-+): 0 found - 170 modified | TOTAL: 698 Iteration Number : 2 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 8 found - 8 modified | TOTAL: 21 pass 2 (xy-): 0 found - 8 modified | TOTAL: 21 pass 1 (yz+): 18 found - 18 modified | TOTAL: 39 pass 2 (yz+): 0 found - 18 modified | TOTAL: 39 pass 1 (yz-): 16 found - 16 modified | TOTAL: 55 pass 2 (yz-): 0 found - 16 modified | TOTAL: 55 pass 1 (xz+): 9 found - 9 modified | TOTAL: 64 pass 2 (xz+): 0 found - 9 modified | TOTAL: 64 pass 1 (xz-): 19 found - 19 modified | TOTAL: 83 pass 2 (xz-): 0 found - 19 modified | TOTAL: 83 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 2 found - 2 modified | TOTAL: 14 pass 2 (+++): 0 found - 2 modified | TOTAL: 14 Iteration Number : 2 pass 1 (++): 12 found - 12 modified | TOTAL: 12 pass 2 (++): 0 found - 12 modified | TOTAL: 12 pass 1 (+-): 9 found - 9 modified | TOTAL: 21 pass 2 (+-): 0 found - 9 modified | TOTAL: 21 pass 1 (--): 4 found - 4 modified | TOTAL: 25 pass 2 (--): 0 found - 4 modified | TOTAL: 25 pass 1 (-+): 2 found - 2 modified | TOTAL: 27 pass 2 (-+): 0 found - 2 modified | TOTAL: 27 Iteration Number : 3 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+): 3 found - 3 modified | TOTAL: 7 pass 2 (yz+): 0 found - 3 modified | TOTAL: 7 pass 1 (yz-): 3 found - 3 modified | TOTAL: 10 pass 2 (yz-): 0 found - 3 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 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 (++): 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 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 1284 (out of 475355: 0.270114) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Oct 27 01:29:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18140; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04428 -0.10535 0.04182 7.25174; 0.09913 1.08872 0.08160 -28.18140; -0.04241 -0.07024 0.99168 12.88991; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1125 (min = 350, max = 1400), aspect = 0.75 (min = 0.10, max = 0.75) need search nearby using seed (126, 116, 94), TAL = (2.0, -34.0, 12.0) talairach voxel to voxel transform 0.94727 0.08862 -0.04724 -3.76308; -0.08882 0.90535 -0.07075 27.07001; 0.03422 0.06792 1.00136 -11.24164; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 116, 94) --> (2.0, -34.0, 12.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (2.00, -34.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -34.00, 12.00) SRC: (104.38, 115.85, 94.46) search lh wm seed point around talairach space (-16.00, -34.00, 12.00), SRC: (138.48, 112.65, 95.69) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Oct 27 01:29:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 1 found - 1 modified | TOTAL: 5 pass 2 (xy-): 0 found - 1 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 2 found - 2 modified | TOTAL: 11 pass 2 (xz+): 0 found - 2 modified | TOTAL: 11 pass 1 (xz-): 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 : 1 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 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 15 (out of 235604: 0.006367) 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: 46 vertices, 55 faces slice 40: 3221 vertices, 3392 faces slice 50: 10744 vertices, 11154 faces slice 60: 20915 vertices, 21358 faces slice 70: 31610 vertices, 32128 faces slice 80: 44852 vertices, 45466 faces slice 90: 58918 vertices, 59594 faces slice 100: 73167 vertices, 73912 faces slice 110: 86153 vertices, 86888 faces slice 120: 98776 vertices, 99590 faces slice 130: 111420 vertices, 112260 faces slice 140: 122814 vertices, 123612 faces slice 150: 132418 vertices, 133212 faces slice 160: 140984 vertices, 141731 faces slice 170: 147284 vertices, 147977 faces slice 180: 152176 vertices, 152844 faces slice 190: 154050 vertices, 154570 faces slice 200: 154060 vertices, 154574 faces slice 210: 154060 vertices, 154574 faces slice 220: 154060 vertices, 154574 faces slice 230: 154060 vertices, 154574 faces slice 240: 154060 vertices, 154574 faces slice 250: 154060 vertices, 154574 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... 154060 voxel in cpt #1: X=-514 [v=154060,e=463722,f=309148] located at (-23.236538, -24.180761, 17.568182) For the whole surface: X=-514 [v=154060,e=463722,f=309148] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri Oct 27 01:30:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 3 found - 3 modified | TOTAL: 8 pass 2 (xz+): 0 found - 3 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 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 (+-): 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 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 = 14 (out of 232763: 0.006015) 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 40: 932 vertices, 1032 faces slice 50: 5807 vertices, 6085 faces slice 60: 14516 vertices, 14941 faces slice 70: 25035 vertices, 25491 faces slice 80: 36193 vertices, 36706 faces slice 90: 48752 vertices, 49306 faces slice 100: 62606 vertices, 63177 faces slice 110: 75841 vertices, 76488 faces slice 120: 88418 vertices, 89031 faces slice 130: 100765 vertices, 101456 faces slice 140: 111672 vertices, 112286 faces slice 150: 121204 vertices, 121808 faces slice 160: 129891 vertices, 130482 faces slice 170: 137361 vertices, 137876 faces slice 180: 142479 vertices, 142943 faces slice 190: 145226 vertices, 145585 faces slice 200: 145424 vertices, 145740 faces slice 210: 145424 vertices, 145740 faces slice 220: 145424 vertices, 145740 faces slice 230: 145424 vertices, 145740 faces slice 240: 145424 vertices, 145740 faces slice 250: 145424 vertices, 145740 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... 145424 voxel in cpt #1: X=-316 [v=145424,e=437220,f=291480] located at (36.298618, -19.734886, 15.450806) For the whole surface: X=-316 [v=145424,e=437220,f=291480] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Oct 27 01:30:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Oct 27 01:30:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 5281 of (5281 5284) to complete... Waiting for PID 5284 of (5281 5284) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (5281 5284) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Oct 27 01:30:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Oct 27 01:30:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 5652 of (5652 5655) to complete... Waiting for PID 5655 of (5652 5655) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.7 mm, total surface area = 77325 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.2 minutes step 000: RMS=0.195 (target=0.015) step 005: RMS=0.156 (target=0.015) step 010: RMS=0.131 (target=0.015) step 015: RMS=0.121 (target=0.015) step 020: RMS=0.114 (target=0.015) step 025: RMS=0.111 (target=0.015) step 030: RMS=0.106 (target=0.015) step 035: RMS=0.104 (target=0.015) step 040: RMS=0.102 (target=0.015) step 045: RMS=0.102 (target=0.015) step 050: RMS=0.102 (target=0.015) step 055: RMS=0.102 (target=0.015) step 060: RMS=0.102 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 36.388468 mris_inflate stimesec 0.068989 mris_inflate ru_maxrss 199188 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26227 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10864 mris_inflate ru_oublock 10880 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 227 mris_inflate ru_nivcsw 3513 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.2 mm, total surface area = 73442 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.1 minutes step 000: RMS=0.188 (target=0.015) step 005: RMS=0.148 (target=0.015) step 010: RMS=0.124 (target=0.015) step 015: RMS=0.113 (target=0.015) step 020: RMS=0.105 (target=0.015) step 025: RMS=0.101 (target=0.015) step 030: RMS=0.097 (target=0.015) step 035: RMS=0.095 (target=0.015) step 040: RMS=0.092 (target=0.015) step 045: RMS=0.092 (target=0.015) step 050: RMS=0.091 (target=0.015) step 055: RMS=0.091 (target=0.015) step 060: RMS=0.091 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 34.187802 mris_inflate stimesec 0.086986 mris_inflate ru_maxrss 187720 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 24381 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10248 mris_inflate ru_oublock 10264 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 33 mris_inflate ru_nivcsw 3467 PIDs (5652 5655) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Oct 27 01:31:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Oct 27 01:31:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 7692 of (7692 7695) to complete... Waiting for PID 7695 of (7692 7695) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.67 (0.00-->10.69) (max @ vno 66919 --> 68531) face area 0.03 +- 0.04 (-0.37-->0.92) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.828, avgs=0 005/300: dt: 0.9000, rms radial error=176.567, avgs=0 010/300: dt: 0.9000, rms radial error=176.008, avgs=0 015/300: dt: 0.9000, rms radial error=175.274, avgs=0 020/300: dt: 0.9000, rms radial error=174.440, avgs=0 025/300: dt: 0.9000, rms radial error=173.548, avgs=0 030/300: dt: 0.9000, rms radial error=172.624, avgs=0 035/300: dt: 0.9000, rms radial error=171.682, avgs=0 040/300: dt: 0.9000, rms radial error=170.732, avgs=0 045/300: dt: 0.9000, rms radial error=169.785, avgs=0 050/300: dt: 0.9000, rms radial error=168.838, avgs=0 055/300: dt: 0.9000, rms radial error=167.894, avgs=0 060/300: dt: 0.9000, rms radial error=166.954, avgs=0 065/300: dt: 0.9000, rms radial error=166.017, avgs=0 070/300: dt: 0.9000, rms radial error=165.084, avgs=0 075/300: dt: 0.9000, rms radial error=164.157, avgs=0 080/300: dt: 0.9000, rms radial error=163.233, avgs=0 085/300: dt: 0.9000, rms radial error=162.314, avgs=0 090/300: dt: 0.9000, rms radial error=161.401, avgs=0 095/300: dt: 0.9000, rms radial error=160.492, avgs=0 100/300: dt: 0.9000, rms radial error=159.589, avgs=0 105/300: dt: 0.9000, rms radial error=158.694, avgs=0 110/300: dt: 0.9000, rms radial error=157.804, avgs=0 115/300: dt: 0.9000, rms radial error=156.918, avgs=0 120/300: dt: 0.9000, rms radial error=156.039, avgs=0 125/300: dt: 0.9000, rms radial error=155.164, avgs=0 130/300: dt: 0.9000, rms radial error=154.294, avgs=0 135/300: dt: 0.9000, rms radial error=153.429, avgs=0 140/300: dt: 0.9000, rms radial error=152.569, avgs=0 145/300: dt: 0.9000, rms radial error=151.713, avgs=0 150/300: dt: 0.9000, rms radial error=150.861, avgs=0 155/300: dt: 0.9000, rms radial error=150.015, avgs=0 160/300: dt: 0.9000, rms radial error=149.173, avgs=0 165/300: dt: 0.9000, rms radial error=148.335, avgs=0 170/300: dt: 0.9000, rms radial error=147.503, avgs=0 175/300: dt: 0.9000, rms radial error=146.674, avgs=0 180/300: dt: 0.9000, rms radial error=145.850, avgs=0 185/300: dt: 0.9000, rms radial error=145.030, avgs=0 190/300: dt: 0.9000, rms radial error=144.215, avgs=0 195/300: dt: 0.9000, rms radial error=143.404, avgs=0 200/300: dt: 0.9000, rms radial error=142.598, avgs=0 205/300: dt: 0.9000, rms radial error=141.796, avgs=0 210/300: dt: 0.9000, rms radial error=140.999, avgs=0 215/300: dt: 0.9000, rms radial error=140.206, avgs=0 220/300: dt: 0.9000, rms radial error=139.417, avgs=0 225/300: dt: 0.9000, rms radial error=138.633, avgs=0 230/300: dt: 0.9000, rms radial error=137.853, avgs=0 235/300: dt: 0.9000, rms radial error=137.078, avgs=0 240/300: dt: 0.9000, rms radial error=136.307, avgs=0 245/300: dt: 0.9000, rms radial error=135.540, avgs=0 250/300: dt: 0.9000, rms radial error=134.777, avgs=0 255/300: dt: 0.9000, rms radial error=134.019, avgs=0 260/300: dt: 0.9000, rms radial error=133.264, avgs=0 265/300: dt: 0.9000, rms radial error=132.514, avgs=0 270/300: dt: 0.9000, rms radial error=131.769, avgs=0 275/300: dt: 0.9000, rms radial error=131.027, avgs=0 280/300: dt: 0.9000, rms radial error=130.290, avgs=0 285/300: dt: 0.9000, rms radial error=129.557, avgs=0 290/300: dt: 0.9000, rms radial error=128.828, avgs=0 295/300: dt: 0.9000, rms radial error=128.103, avgs=0 300/300: dt: 0.9000, rms radial error=127.383, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18281.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00022 epoch 2 (K=40.0), pass 1, starting sse = 3316.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00058 epoch 3 (K=160.0), pass 1, starting sse = 496.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00386 epoch 4 (K=640.0), pass 1, starting sse = 99.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00693 final distance error %29.18 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.12 hours mris_sphere utimesec 226.274601 mris_sphere stimesec 0.085986 mris_sphere ru_maxrss 199392 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 26276 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 10864 mris_sphere ru_oublock 10904 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 243 mris_sphere ru_nivcsw 21961 FSRUNTIME@ mris_sphere 0.1228 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.64 (0.00-->15.58) (max @ vno 79516 --> 79529) face area 0.03 +- 0.04 (-0.91-->1.37) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.323... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.367, avgs=0 005/300: dt: 0.9000, rms radial error=176.106, avgs=0 010/300: dt: 0.9000, rms radial error=175.551, avgs=0 015/300: dt: 0.9000, rms radial error=174.822, avgs=0 020/300: dt: 0.9000, rms radial error=173.991, avgs=0 025/300: dt: 0.9000, rms radial error=173.101, avgs=0 030/300: dt: 0.9000, rms radial error=172.178, avgs=0 035/300: dt: 0.9000, rms radial error=171.239, avgs=0 040/300: dt: 0.9000, rms radial error=170.293, avgs=0 045/300: dt: 0.9000, rms radial error=169.345, avgs=0 050/300: dt: 0.9000, rms radial error=168.399, avgs=0 055/300: dt: 0.9000, rms radial error=167.455, avgs=0 060/300: dt: 0.9000, rms radial error=166.515, avgs=0 065/300: dt: 0.9000, rms radial error=165.579, avgs=0 070/300: dt: 0.9000, rms radial error=164.648, avgs=0 075/300: dt: 0.9000, rms radial error=163.721, avgs=0 080/300: dt: 0.9000, rms radial error=162.800, avgs=0 085/300: dt: 0.9000, rms radial error=161.883, avgs=0 090/300: dt: 0.9000, rms radial error=160.970, avgs=0 095/300: dt: 0.9000, rms radial error=160.062, avgs=0 100/300: dt: 0.9000, rms radial error=159.159, avgs=0 105/300: dt: 0.9000, rms radial error=158.261, avgs=0 110/300: dt: 0.9000, rms radial error=157.369, avgs=0 115/300: dt: 0.9000, rms radial error=156.481, avgs=0 120/300: dt: 0.9000, rms radial error=155.598, avgs=0 125/300: dt: 0.9000, rms radial error=154.720, avgs=0 130/300: dt: 0.9000, rms radial error=153.847, avgs=0 135/300: dt: 0.9000, rms radial error=152.979, avgs=0 140/300: dt: 0.9000, rms radial error=152.115, avgs=0 145/300: dt: 0.9000, rms radial error=151.256, avgs=0 150/300: dt: 0.9000, rms radial error=150.402, avgs=0 155/300: dt: 0.9000, rms radial error=149.553, avgs=0 160/300: dt: 0.9000, rms radial error=148.709, avgs=0 165/300: dt: 0.9000, rms radial error=147.869, avgs=0 170/300: dt: 0.9000, rms radial error=147.035, avgs=0 175/300: dt: 0.9000, rms radial error=146.205, avgs=0 180/300: dt: 0.9000, rms radial error=145.379, avgs=0 185/300: dt: 0.9000, rms radial error=144.558, avgs=0 190/300: dt: 0.9000, rms radial error=143.742, avgs=0 195/300: dt: 0.9000, rms radial error=142.930, avgs=0 200/300: dt: 0.9000, rms radial error=142.123, avgs=0 205/300: dt: 0.9000, rms radial error=141.321, avgs=0 210/300: dt: 0.9000, rms radial error=140.523, avgs=0 215/300: dt: 0.9000, rms radial error=139.729, avgs=0 220/300: dt: 0.9000, rms radial error=138.940, avgs=0 225/300: dt: 0.9000, rms radial error=138.156, avgs=0 230/300: dt: 0.9000, rms radial error=137.376, avgs=0 235/300: dt: 0.9000, rms radial error=136.600, avgs=0 240/300: dt: 0.9000, rms radial error=135.829, avgs=0 245/300: dt: 0.9000, rms radial error=135.063, avgs=0 250/300: dt: 0.9000, rms radial error=134.300, avgs=0 255/300: dt: 0.9000, rms radial error=133.542, avgs=0 260/300: dt: 0.9000, rms radial error=132.789, avgs=0 265/300: dt: 0.9000, rms radial error=132.039, avgs=0 270/300: dt: 0.9000, rms radial error=131.294, avgs=0 275/300: dt: 0.9000, rms radial error=130.553, avgs=0 280/300: dt: 0.9000, rms radial error=129.816, avgs=0 285/300: dt: 0.9000, rms radial error=129.083, avgs=0 290/300: dt: 0.9000, rms radial error=128.355, avgs=0 295/300: dt: 0.9000, rms radial error=127.630, avgs=0 300/300: dt: 0.9000, rms radial error=126.910, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17067.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2983.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00023 epoch 3 (K=160.0), pass 1, starting sse = 390.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00127 epoch 4 (K=640.0), pass 1, starting sse = 71.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00561 final distance error %26.96 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours mris_sphere utimesec 215.925174 mris_sphere stimesec 0.078987 mris_sphere ru_maxrss 187916 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 24428 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 10248 mris_sphere ru_oublock 10288 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 260 mris_sphere ru_nivcsw 21716 FSRUNTIME@ mris_sphere 0.1199 hours 1 threads PIDs (7692 7695) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Fri Oct 27 01:38:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri Oct 27 01:38:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri Oct 27 01:38:53 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 lh #@# Fix Topology rh Fri Oct 27 01:38:53 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 rh Waiting for PID 20548 of (20548 20551) to complete... Waiting for PID 20551 of (20548 20551) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 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=-514 (nv=154060, nf=309148, ne=463722, g=258) 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... 54267 ambiguous faces found in tessellation segmenting defects... 154 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 45 into 35 -merging segment 56 into 35 -merging segment 58 into 35 -merging segment 80 into 35 -merging segment 103 into 35 -merging segment 90 into 35 -merging segment 70 into 62 -merging segment 68 into 65 -merging segment 91 into 89 -merging segment 118 into 99 -merging segment 114 into 109 -merging segment 115 into 109 -merging segment 152 into 149 141 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4716 (-4.7358) -vertex loglikelihood: -6.5776 (-3.2888) -normal dot loglikelihood: -3.5519 (-3.5519) -quad curv loglikelihood: -6.2359 (-3.1179) Total Loglikelihood : -25.8369 CORRECTING DEFECT 0 (vertices=1852, convex hull=655, v0=82) XL defect detected... After retessellation of defect 0 (v0=82), euler #=-131 (123371,361991,238489) : difference with theory (-138) = -7 CORRECTING DEFECT 1 (vertices=26, convex hull=32, v0=125) After retessellation of defect 1 (v0=125), euler #=-130 (123374,362009,238505) : difference with theory (-137) = -7 CORRECTING DEFECT 2 (vertices=52, convex hull=74, v0=1269) After retessellation of defect 2 (v0=1269), euler #=-129 (123388,362080,238563) : difference with theory (-136) = -7 CORRECTING DEFECT 3 (vertices=31, convex hull=53, v0=1455) After retessellation of defect 3 (v0=1455), euler #=-128 (123395,362124,238601) : difference with theory (-135) = -7 CORRECTING DEFECT 4 (vertices=73, convex hull=57, v0=1747) After retessellation of defect 4 (v0=1747), euler #=-127 (123403,362168,238638) : difference with theory (-134) = -7 CORRECTING DEFECT 5 (vertices=20, convex hull=57, v0=1976) After retessellation of defect 5 (v0=1976), euler #=-126 (123415,362226,238685) : difference with theory (-133) = -7 CORRECTING DEFECT 6 (vertices=26, convex hull=62, v0=3756) After retessellation of defect 6 (v0=3756), euler #=-125 (123424,362276,238727) : difference with theory (-132) = -7 CORRECTING DEFECT 7 (vertices=175, convex hull=168, v0=5442) After retessellation of defect 7 (v0=5442), euler #=-125 (123500,362595,238970) : difference with theory (-131) = -6 CORRECTING DEFECT 8 (vertices=48, convex hull=33, v0=5470) After retessellation of defect 8 (v0=5470), euler #=-124 (123503,362617,238990) : difference with theory (-130) = -6 CORRECTING DEFECT 9 (vertices=105, convex hull=140, v0=5963) After retessellation of defect 9 (v0=5963), euler #=-123 (123566,362870,239181) : difference with theory (-129) = -6 CORRECTING DEFECT 10 (vertices=68, convex hull=95, v0=6999) After retessellation of defect 10 (v0=6999), euler #=-122 (123590,362979,239267) : difference with theory (-128) = -6 CORRECTING DEFECT 11 (vertices=172, convex hull=141, v0=7015) After retessellation of defect 11 (v0=7015), euler #=-122 (123639,363204,239443) : difference with theory (-127) = -5 CORRECTING DEFECT 12 (vertices=5, convex hull=25, v0=7139) After retessellation of defect 12 (v0=7139), euler #=-121 (123639,363209,239449) : difference with theory (-126) = -5 CORRECTING DEFECT 13 (vertices=281, convex hull=138, v0=7227) After retessellation of defect 13 (v0=7227), euler #=-120 (123709,363481,239652) : difference with theory (-125) = -5 CORRECTING DEFECT 14 (vertices=32, convex hull=76, v0=7548) After retessellation of defect 14 (v0=7548), euler #=-119 (123730,363573,239724) : difference with theory (-124) = -5 CORRECTING DEFECT 15 (vertices=52, convex hull=81, v0=8730) After retessellation of defect 15 (v0=8730), euler #=-118 (123765,363709,239826) : difference with theory (-123) = -5 CORRECTING DEFECT 16 (vertices=103, convex hull=34, v0=9334) After retessellation of defect 16 (v0=9334), euler #=-117 (123773,363743,239853) : difference with theory (-122) = -5 CORRECTING DEFECT 17 (vertices=50, convex hull=38, v0=9386) After retessellation of defect 17 (v0=9386), euler #=-116 (123776,363763,239871) : difference with theory (-121) = -5 CORRECTING DEFECT 18 (vertices=366, convex hull=190, v0=9451) After retessellation of defect 18 (v0=9451), euler #=-115 (123859,364115,240141) : difference with theory (-120) = -5 CORRECTING DEFECT 19 (vertices=157, convex hull=108, v0=10502) After retessellation of defect 19 (v0=10502), euler #=-114 (123886,364246,240246) : difference with theory (-119) = -5 CORRECTING DEFECT 20 (vertices=35, convex hull=23, v0=10667) After retessellation of defect 20 (v0=10667), euler #=-113 (123890,364264,240261) : difference with theory (-118) = -5 CORRECTING DEFECT 21 (vertices=48, convex hull=91, v0=10861) After retessellation of defect 21 (v0=10861), euler #=-112 (123903,364341,240326) : difference with theory (-117) = -5 CORRECTING DEFECT 22 (vertices=100, convex hull=87, v0=12285) After retessellation of defect 22 (v0=12285), euler #=-111 (123943,364496,240442) : difference with theory (-116) = -5 CORRECTING DEFECT 23 (vertices=36, convex hull=78, v0=12718) After retessellation of defect 23 (v0=12718), euler #=-110 (123959,364576,240507) : difference with theory (-115) = -5 CORRECTING DEFECT 24 (vertices=18, convex hull=46, v0=12777) After retessellation of defect 24 (v0=12777), euler #=-109 (123968,364619,240542) : difference with theory (-114) = -5 CORRECTING DEFECT 25 (vertices=33, convex hull=63, v0=13514) After retessellation of defect 25 (v0=13514), euler #=-108 (123990,364708,240610) : difference with theory (-113) = -5 CORRECTING DEFECT 26 (vertices=52, convex hull=45, v0=14436) After retessellation of defect 26 (v0=14436), euler #=-107 (123998,364749,240644) : difference with theory (-112) = -5 CORRECTING DEFECT 27 (vertices=36, convex hull=81, v0=15705) After retessellation of defect 27 (v0=15705), euler #=-106 (124016,364837,240715) : difference with theory (-111) = -5 CORRECTING DEFECT 28 (vertices=6, convex hull=25, v0=16080) After retessellation of defect 28 (v0=16080), euler #=-105 (124016,364846,240725) : difference with theory (-110) = -5 CORRECTING DEFECT 29 (vertices=332, convex hull=188, v0=16391) After retessellation of defect 29 (v0=16391), euler #=-104 (124117,365233,241012) : difference with theory (-109) = -5 CORRECTING DEFECT 30 (vertices=49, convex hull=50, v0=17596) After retessellation of defect 30 (v0=17596), euler #=-103 (124123,365274,241048) : difference with theory (-108) = -5 CORRECTING DEFECT 31 (vertices=5, convex hull=26, v0=18681) After retessellation of defect 31 (v0=18681), euler #=-102 (124123,365280,241055) : difference with theory (-107) = -5 CORRECTING DEFECT 32 (vertices=44, convex hull=77, v0=18759) After retessellation of defect 32 (v0=18759), euler #=-101 (124144,365374,241129) : difference with theory (-106) = -5 CORRECTING DEFECT 33 (vertices=18, convex hull=60, v0=19375) After retessellation of defect 33 (v0=19375), euler #=-100 (124155,365430,241175) : difference with theory (-105) = -5 CORRECTING DEFECT 34 (vertices=40, convex hull=36, v0=19673) After retessellation of defect 34 (v0=19673), euler #=-99 (124159,365459,241201) : difference with theory (-104) = -5 CORRECTING DEFECT 35 (vertices=13196, convex hull=5172, v0=20537) XL defect detected... After retessellation of defect 35 (v0=20537), euler #=-101 (127943,379731,251687) : difference with theory (-103) = -2 CORRECTING DEFECT 36 (vertices=164, convex hull=166, v0=21399) After retessellation of defect 36 (v0=21399), euler #=-100 (128010,380009,251899) : difference with theory (-102) = -2 CORRECTING DEFECT 37 (vertices=25, convex hull=24, v0=21737) After retessellation of defect 37 (v0=21737), euler #=-99 (128011,380020,251910) : difference with theory (-101) = -2 CORRECTING DEFECT 38 (vertices=5, convex hull=18, v0=23692) After retessellation of defect 38 (v0=23692), euler #=-98 (128011,380024,251915) : difference with theory (-100) = -2 CORRECTING DEFECT 39 (vertices=35, convex hull=69, v0=23838) After retessellation of defect 39 (v0=23838), euler #=-97 (128029,380102,251976) : difference with theory (-99) = -2 CORRECTING DEFECT 40 (vertices=107, convex hull=99, v0=24305) After retessellation of defect 40 (v0=24305), euler #=-96 (128086,380319,252137) : difference with theory (-98) = -2 CORRECTING DEFECT 41 (vertices=197, convex hull=126, v0=24688) After retessellation of defect 41 (v0=24688), euler #=-95 (128120,380487,252272) : difference with theory (-97) = -2 CORRECTING DEFECT 42 (vertices=120, convex hull=147, v0=24935) After retessellation of defect 42 (v0=24935), euler #=-94 (128172,380705,252439) : difference with theory (-96) = -2 CORRECTING DEFECT 43 (vertices=22, convex hull=51, v0=25034) After retessellation of defect 43 (v0=25034), euler #=-93 (128183,380758,252482) : difference with theory (-95) = -2 CORRECTING DEFECT 44 (vertices=69, convex hull=73, v0=25579) After retessellation of defect 44 (v0=25579), euler #=-92 (128203,380847,252552) : difference with theory (-94) = -2 CORRECTING DEFECT 45 (vertices=22, convex hull=24, v0=28815) After retessellation of defect 45 (v0=28815), euler #=-91 (128208,380871,252572) : difference with theory (-93) = -2 CORRECTING DEFECT 46 (vertices=153, convex hull=156, v0=29415) After retessellation of defect 46 (v0=29415), euler #=-90 (128260,381103,252753) : difference with theory (-92) = -2 CORRECTING DEFECT 47 (vertices=27, convex hull=67, v0=30636) After retessellation of defect 47 (v0=30636), euler #=-89 (128272,381163,252802) : difference with theory (-91) = -2 CORRECTING DEFECT 48 (vertices=193, convex hull=67, v0=30886) After retessellation of defect 48 (v0=30886), euler #=-88 (128294,381257,252875) : difference with theory (-90) = -2 CORRECTING DEFECT 49 (vertices=37, convex hull=66, v0=31503) After retessellation of defect 49 (v0=31503), euler #=-87 (128313,381343,252943) : difference with theory (-89) = -2 CORRECTING DEFECT 50 (vertices=72, convex hull=107, v0=31975) After retessellation of defect 50 (v0=31975), euler #=-86 (128349,381498,253063) : difference with theory (-88) = -2 CORRECTING DEFECT 51 (vertices=29, convex hull=73, v0=33178) After retessellation of defect 51 (v0=33178), euler #=-85 (128366,381578,253127) : difference with theory (-87) = -2 CORRECTING DEFECT 52 (vertices=78, convex hull=31, v0=33827) After retessellation of defect 52 (v0=33827), euler #=-84 (128368,381597,253145) : difference with theory (-86) = -2 CORRECTING DEFECT 53 (vertices=126, convex hull=108, v0=35543) After retessellation of defect 53 (v0=35543), euler #=-83 (128399,381742,253260) : difference with theory (-85) = -2 CORRECTING DEFECT 54 (vertices=41, convex hull=69, v0=38998) After retessellation of defect 54 (v0=38998), euler #=-82 (128412,381810,253316) : difference with theory (-84) = -2 CORRECTING DEFECT 55 (vertices=187, convex hull=193, v0=43442) After retessellation of defect 55 (v0=43442), euler #=-81 (128475,382087,253531) : difference with theory (-83) = -2 CORRECTING DEFECT 56 (vertices=31, convex hull=48, v0=44394) After retessellation of defect 56 (v0=44394), euler #=-80 (128492,382153,253581) : difference with theory (-82) = -2 CORRECTING DEFECT 57 (vertices=42, convex hull=55, v0=45218) After retessellation of defect 57 (v0=45218), euler #=-79 (128514,382241,253648) : difference with theory (-81) = -2 CORRECTING DEFECT 58 (vertices=18, convex hull=33, v0=45302) After retessellation of defect 58 (v0=45302), euler #=-78 (128517,382262,253667) : difference with theory (-80) = -2 CORRECTING DEFECT 59 (vertices=1238, convex hull=639, v0=45521) XL defect detected... After retessellation of defect 59 (v0=45521), euler #=-80 (128893,383735,254762) : difference with theory (-79) = 1 CORRECTING DEFECT 60 (vertices=46, convex hull=37, v0=46122) After retessellation of defect 60 (v0=46122), euler #=-79 (128898,383764,254787) : difference with theory (-78) = 1 CORRECTING DEFECT 61 (vertices=25, convex hull=54, v0=46592) After retessellation of defect 61 (v0=46592), euler #=-78 (128912,383824,254834) : difference with theory (-77) = 1 CORRECTING DEFECT 62 (vertices=104, convex hull=122, v0=47545) After retessellation of defect 62 (v0=47545), euler #=-76 (128934,383951,254941) : difference with theory (-76) = 0 CORRECTING DEFECT 63 (vertices=52, convex hull=34, v0=48329) After retessellation of defect 63 (v0=48329), euler #=-75 (128942,383989,254972) : difference with theory (-75) = 0 CORRECTING DEFECT 64 (vertices=38, convex hull=39, v0=48353) After retessellation of defect 64 (v0=48353), euler #=-74 (128954,384041,255013) : difference with theory (-74) = 0 CORRECTING DEFECT 65 (vertices=29, convex hull=78, v0=49949) After retessellation of defect 65 (v0=49949), euler #=-73 (128972,384132,255087) : difference with theory (-73) = 0 CORRECTING DEFECT 66 (vertices=95, convex hull=164, v0=54082) After retessellation of defect 66 (v0=54082), euler #=-72 (129001,384292,255219) : difference with theory (-72) = 0 CORRECTING DEFECT 67 (vertices=21, convex hull=27, v0=55783) After retessellation of defect 67 (v0=55783), euler #=-71 (129002,384303,255230) : difference with theory (-71) = 0 CORRECTING DEFECT 68 (vertices=46, convex hull=67, v0=56489) After retessellation of defect 68 (v0=56489), euler #=-70 (129033,384425,255322) : difference with theory (-70) = 0 CORRECTING DEFECT 69 (vertices=41, convex hull=66, v0=62822) After retessellation of defect 69 (v0=62822), euler #=-69 (129049,384497,255379) : difference with theory (-69) = 0 CORRECTING DEFECT 70 (vertices=29, convex hull=31, v0=62930) After retessellation of defect 70 (v0=62930), euler #=-68 (129052,384519,255399) : difference with theory (-68) = 0 CORRECTING DEFECT 71 (vertices=34, convex hull=33, v0=63183) After retessellation of defect 71 (v0=63183), euler #=-67 (129055,384538,255416) : difference with theory (-67) = 0 CORRECTING DEFECT 72 (vertices=46, convex hull=94, v0=63224) After retessellation of defect 72 (v0=63224), euler #=-66 (129086,384670,255518) : difference with theory (-66) = 0 CORRECTING DEFECT 73 (vertices=135, convex hull=74, v0=64348) After retessellation of defect 73 (v0=64348), euler #=-66 (129111,384782,255605) : difference with theory (-65) = 1 CORRECTING DEFECT 74 (vertices=43, convex hull=53, v0=69405) After retessellation of defect 74 (v0=69405), euler #=-65 (129124,384840,255651) : difference with theory (-64) = 1 CORRECTING DEFECT 75 (vertices=22, convex hull=17, v0=72847) After retessellation of defect 75 (v0=72847), euler #=-64 (129127,384854,255663) : difference with theory (-63) = 1 CORRECTING DEFECT 76 (vertices=41, convex hull=82, v0=73101) After retessellation of defect 76 (v0=73101), euler #=-63 (129139,384932,255730) : difference with theory (-62) = 1 CORRECTING DEFECT 77 (vertices=96, convex hull=102, v0=73351) After retessellation of defect 77 (v0=73351), euler #=-62 (129192,385137,255883) : difference with theory (-61) = 1 CORRECTING DEFECT 78 (vertices=29, convex hull=63, v0=73833) After retessellation of defect 78 (v0=73833), euler #=-61 (129209,385215,255945) : difference with theory (-60) = 1 CORRECTING DEFECT 79 (vertices=33, convex hull=68, v0=73866) After retessellation of defect 79 (v0=73866), euler #=-60 (129231,385307,256016) : difference with theory (-59) = 1 CORRECTING DEFECT 80 (vertices=98, convex hull=48, v0=74595) After retessellation of defect 80 (v0=74595), euler #=-59 (129240,385356,256057) : difference with theory (-58) = 1 CORRECTING DEFECT 81 (vertices=10, convex hull=18, v0=76584) After retessellation of defect 81 (v0=76584), euler #=-58 (129241,385366,256067) : difference with theory (-57) = 1 CORRECTING DEFECT 82 (vertices=108, convex hull=135, v0=78474) After retessellation of defect 82 (v0=78474), euler #=-57 (129251,385457,256149) : difference with theory (-56) = 1 CORRECTING DEFECT 83 (vertices=41, convex hull=53, v0=81006) After retessellation of defect 83 (v0=81006), euler #=-55 (129260,385507,256192) : difference with theory (-55) = 0 CORRECTING DEFECT 84 (vertices=48, convex hull=61, v0=84591) After retessellation of defect 84 (v0=84591), euler #=-54 (129285,385609,256270) : difference with theory (-54) = 0 CORRECTING DEFECT 85 (vertices=39, convex hull=44, v0=87157) After retessellation of defect 85 (v0=87157), euler #=-53 (129291,385642,256298) : difference with theory (-53) = 0 CORRECTING DEFECT 86 (vertices=56, convex hull=106, v0=88480) After retessellation of defect 86 (v0=88480), euler #=-52 (129318,385777,256407) : difference with theory (-52) = 0 CORRECTING DEFECT 87 (vertices=113, convex hull=110, v0=88544) After retessellation of defect 87 (v0=88544), euler #=-51 (129359,385960,256550) : difference with theory (-51) = 0 CORRECTING DEFECT 88 (vertices=40, convex hull=61, v0=88576) After retessellation of defect 88 (v0=88576), euler #=-50 (129381,386046,256615) : difference with theory (-50) = 0 CORRECTING DEFECT 89 (vertices=166, convex hull=49, v0=89740) After retessellation of defect 89 (v0=89740), euler #=-49 (129399,386121,256673) : difference with theory (-49) = 0 CORRECTING DEFECT 90 (vertices=129, convex hull=206, v0=90255) After retessellation of defect 90 (v0=90255), euler #=-48 (129490,386497,256959) : difference with theory (-48) = 0 CORRECTING DEFECT 91 (vertices=1101, convex hull=275, v0=92246) After retessellation of defect 91 (v0=92246), euler #=-48 (129746,387426,257632) : difference with theory (-47) = 1 CORRECTING DEFECT 92 (vertices=21, convex hull=55, v0=94279) After retessellation of defect 92 (v0=94279), euler #=-47 (129756,387477,257674) : difference with theory (-46) = 1 CORRECTING DEFECT 93 (vertices=66, convex hull=102, v0=94848) After retessellation of defect 93 (v0=94848), euler #=-46 (129794,387636,257796) : difference with theory (-45) = 1 CORRECTING DEFECT 94 (vertices=24, convex hull=66, v0=96667) After retessellation of defect 94 (v0=96667), euler #=-45 (129803,387686,257838) : difference with theory (-44) = 1 CORRECTING DEFECT 95 (vertices=72, convex hull=95, v0=99039) After retessellation of defect 95 (v0=99039), euler #=-44 (129826,387797,257927) : difference with theory (-43) = 1 CORRECTING DEFECT 96 (vertices=2594, convex hull=529, v0=99867) XL defect detected... After retessellation of defect 96 (v0=99867), euler #=-44 (130271,389439,259124) : difference with theory (-42) = 2 CORRECTING DEFECT 97 (vertices=38, convex hull=62, v0=102000) After retessellation of defect 97 (v0=102000), euler #=-43 (130281,389494,259170) : difference with theory (-41) = 2 CORRECTING DEFECT 98 (vertices=100, convex hull=37, v0=103995) After retessellation of defect 98 (v0=103995), euler #=-42 (130292,389544,259210) : difference with theory (-40) = 2 CORRECTING DEFECT 99 (vertices=5, convex hull=15, v0=106471) After retessellation of defect 99 (v0=106471), euler #=-41 (130293,389551,259217) : difference with theory (-39) = 2 CORRECTING DEFECT 100 (vertices=243, convex hull=260, v0=107059) After retessellation of defect 100 (v0=107059), euler #=-38 (130386,389954,259530) : difference with theory (-38) = 0 CORRECTING DEFECT 101 (vertices=38, convex hull=59, v0=109721) After retessellation of defect 101 (v0=109721), euler #=-37 (130395,390006,259574) : difference with theory (-37) = 0 CORRECTING DEFECT 102 (vertices=125, convex hull=43, v0=109975) After retessellation of defect 102 (v0=109975), euler #=-36 (130404,390048,259608) : difference with theory (-36) = 0 CORRECTING DEFECT 103 (vertices=19, convex hull=25, v0=110007) After retessellation of defect 103 (v0=110007), euler #=-35 (130406,390061,259620) : difference with theory (-35) = 0 CORRECTING DEFECT 104 (vertices=44, convex hull=71, v0=111755) After retessellation of defect 104 (v0=111755), euler #=-34 (130441,390198,259723) : difference with theory (-34) = 0 CORRECTING DEFECT 105 (vertices=38, convex hull=60, v0=113772) After retessellation of defect 105 (v0=113772), euler #=-33 (130460,390277,259784) : difference with theory (-33) = 0 CORRECTING DEFECT 106 (vertices=26, convex hull=34, v0=114689) After retessellation of defect 106 (v0=114689), euler #=-32 (130464,390300,259804) : difference with theory (-32) = 0 CORRECTING DEFECT 107 (vertices=555, convex hull=128, v0=116310) After retessellation of defect 107 (v0=116310), euler #=-32 (130566,390670,260072) : difference with theory (-31) = 1 CORRECTING DEFECT 108 (vertices=51, convex hull=96, v0=119588) After retessellation of defect 108 (v0=119588), euler #=-31 (130598,390808,260179) : difference with theory (-30) = 1 CORRECTING DEFECT 109 (vertices=73, convex hull=79, v0=120388) After retessellation of defect 109 (v0=120388), euler #=-30 (130631,390939,260278) : difference with theory (-29) = 1 CORRECTING DEFECT 110 (vertices=102, convex hull=39, v0=122413) After retessellation of defect 110 (v0=122413), euler #=-29 (130644,390994,260321) : difference with theory (-28) = 1 CORRECTING DEFECT 111 (vertices=40, convex hull=22, v0=124223) After retessellation of defect 111 (v0=124223), euler #=-28 (130648,391011,260335) : difference with theory (-27) = 1 CORRECTING DEFECT 112 (vertices=59, convex hull=33, v0=124257) After retessellation of defect 112 (v0=124257), euler #=-27 (130654,391040,260359) : difference with theory (-26) = 1 CORRECTING DEFECT 113 (vertices=28, convex hull=25, v0=125545) After retessellation of defect 113 (v0=125545), euler #=-26 (130656,391055,260373) : difference with theory (-25) = 1 CORRECTING DEFECT 114 (vertices=477, convex hull=65, v0=125835) After retessellation of defect 114 (v0=125835), euler #=-25 (130673,391132,260434) : difference with theory (-24) = 1 CORRECTING DEFECT 115 (vertices=159, convex hull=136, v0=128208) After retessellation of defect 115 (v0=128208), euler #=-24 (130737,391388,260627) : difference with theory (-23) = 1 CORRECTING DEFECT 116 (vertices=85, convex hull=134, v0=130564) After retessellation of defect 116 (v0=130564), euler #=-23 (130774,391559,260762) : difference with theory (-22) = 1 CORRECTING DEFECT 117 (vertices=13, convex hull=23, v0=131053) After retessellation of defect 117 (v0=131053), euler #=-22 (130775,391568,260771) : difference with theory (-21) = 1 CORRECTING DEFECT 118 (vertices=317, convex hull=107, v0=133167) After retessellation of defect 118 (v0=133167), euler #=-21 (130813,391733,260899) : difference with theory (-20) = 1 CORRECTING DEFECT 119 (vertices=36, convex hull=20, v0=133217) After retessellation of defect 119 (v0=133217), euler #=-20 (130813,391741,260908) : difference with theory (-19) = 1 CORRECTING DEFECT 120 (vertices=158, convex hull=97, v0=136084) After retessellation of defect 120 (v0=136084), euler #=-19 (130825,391817,260973) : difference with theory (-18) = 1 CORRECTING DEFECT 121 (vertices=46, convex hull=34, v0=137485) After retessellation of defect 121 (v0=137485), euler #=-18 (130830,391844,260996) : difference with theory (-17) = 1 CORRECTING DEFECT 122 (vertices=360, convex hull=176, v0=138259) After retessellation of defect 122 (v0=138259), euler #=-17 (130933,392236,261286) : difference with theory (-16) = 1 CORRECTING DEFECT 123 (vertices=40, convex hull=75, v0=139330) After retessellation of defect 123 (v0=139330), euler #=-16 (130948,392311,261347) : difference with theory (-15) = 1 CORRECTING DEFECT 124 (vertices=41, convex hull=65, v0=140290) After retessellation of defect 124 (v0=140290), euler #=-15 (130970,392404,261419) : difference with theory (-14) = 1 CORRECTING DEFECT 125 (vertices=85, convex hull=89, v0=140650) After retessellation of defect 125 (v0=140650), euler #=-14 (131005,392544,261525) : difference with theory (-13) = 1 CORRECTING DEFECT 126 (vertices=33, convex hull=69, v0=141039) After retessellation of defect 126 (v0=141039), euler #=-13 (131018,392611,261580) : difference with theory (-12) = 1 CORRECTING DEFECT 127 (vertices=44, convex hull=94, v0=142386) After retessellation of defect 127 (v0=142386), euler #=-12 (131047,392741,261682) : difference with theory (-11) = 1 CORRECTING DEFECT 128 (vertices=51, convex hull=108, v0=142527) After retessellation of defect 128 (v0=142527), euler #=-11 (131065,392840,261764) : difference with theory (-10) = 1 CORRECTING DEFECT 129 (vertices=43, convex hull=77, v0=142873) After retessellation of defect 129 (v0=142873), euler #=-10 (131077,392905,261818) : difference with theory (-9) = 1 CORRECTING DEFECT 130 (vertices=30, convex hull=18, v0=143060) After retessellation of defect 130 (v0=143060), euler #=-9 (131077,392910,261824) : difference with theory (-8) = 1 CORRECTING DEFECT 131 (vertices=34, convex hull=27, v0=145650) After retessellation of defect 131 (v0=145650), euler #=-8 (131078,392924,261838) : difference with theory (-7) = 1 CORRECTING DEFECT 132 (vertices=58, convex hull=106, v0=147022) After retessellation of defect 132 (v0=147022), euler #=-7 (131102,393048,261939) : difference with theory (-6) = 1 CORRECTING DEFECT 133 (vertices=34, convex hull=84, v0=147314) After retessellation of defect 133 (v0=147314), euler #=-6 (131116,393125,262003) : difference with theory (-5) = 1 CORRECTING DEFECT 134 (vertices=63, convex hull=50, v0=147590) After retessellation of defect 134 (v0=147590), euler #=-5 (131122,393161,262034) : difference with theory (-4) = 1 CORRECTING DEFECT 135 (vertices=179, convex hull=48, v0=150295) After retessellation of defect 135 (v0=150295), euler #=-4 (131132,393212,262076) : difference with theory (-3) = 1 CORRECTING DEFECT 136 (vertices=23, convex hull=71, v0=151271) After retessellation of defect 136 (v0=151271), euler #=-3 (131144,393272,262125) : difference with theory (-2) = 1 CORRECTING DEFECT 137 (vertices=64, convex hull=60, v0=151636) After retessellation of defect 137 (v0=151636), euler #=-1 (131150,393312,262161) : difference with theory (-1) = 0 CORRECTING DEFECT 138 (vertices=291, convex hull=145, v0=151952) After retessellation of defect 138 (v0=151952), euler #=0 (131214,393571,262357) : difference with theory (0) = 0 CORRECTING DEFECT 139 (vertices=60, convex hull=87, v0=152760) After retessellation of defect 139 (v0=152760), euler #=1 (131237,393678,262442) : difference with theory (1) = 0 CORRECTING DEFECT 140 (vertices=95, convex hull=63, v0=153708) After retessellation of defect 140 (v0=153708), euler #=2 (131248,393738,262492) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.91 +- 0.38 (0.01-->19.97) (max @ vno 57431 --> 132570) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.91 +- 0.38 (0.01-->19.97) (max @ vno 57431 --> 132570) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 441 mutations (36.2%), 777 crossovers (63.8%), 1846 vertices were eliminated building final representation... 22812 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=131248, nf=262492, ne=393738, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 3066.3 minutes 0 defective edges removing intersecting faces 000: 3001 intersecting 001: 458 intersecting 002: 214 intersecting 003: 180 intersecting 004: 172 intersecting 005: 129 intersecting 006: 119 intersecting 007: 102 intersecting expanding nbhd size to 2 008: 109 intersecting 009: 78 intersecting 010: 45 intersecting 011: 35 intersecting 012: 27 intersecting 013: 16 intersecting expanding nbhd size to 3 014: 30 intersecting 015: 6 intersecting expanding nbhd size to 4 016: 7 intersecting 017: 3 intersecting 018: 2 intersecting expanding nbhd size to 5 019: 2 intersecting mris_fix_topology utimesec 173119.689806 mris_fix_topology stimesec 17.504338 mris_fix_topology ru_maxrss 2641484 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 567349 mris_fix_topology ru_majflt 19 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 77160 mris_fix_topology ru_oublock 13712 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 484 mris_fix_topology ru_nivcsw 1468749 FSRUNTIME@ mris_fix_topology lh 51.1058 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050418 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=-316 (nv=145424, nf=291480, ne=437220, g=159) 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... 35363 ambiguous faces found in tessellation segmenting defects... 120 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 6 into 3 -merging segment 8 into 5 -merging segment 14 into 7 -merging segment 22 into 7 -merging segment 17 into 15 -merging segment 24 into 15 -merging segment 46 into 38 -merging segment 73 into 72 -merging segment 90 into 72 -merging segment 94 into 72 -merging segment 86 into 77 108 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5619 (-4.7809) -vertex loglikelihood: -6.6352 (-3.3176) -normal dot loglikelihood: -3.5189 (-3.5189) -quad curv loglikelihood: -6.2410 (-3.1205) Total Loglikelihood : -25.9569 CORRECTING DEFECT 0 (vertices=512, convex hull=292, v0=0) After retessellation of defect 0 (v0=0), euler #=-110 (125182,370015,244723) : difference with theory (-105) = 5 CORRECTING DEFECT 1 (vertices=35, convex hull=72, v0=348) After retessellation of defect 1 (v0=348), euler #=-109 (125203,370109,244797) : difference with theory (-104) = 5 CORRECTING DEFECT 2 (vertices=234, convex hull=215, v0=515) After retessellation of defect 2 (v0=515), euler #=-107 (125288,370482,245087) : difference with theory (-103) = 4 CORRECTING DEFECT 3 (vertices=35, convex hull=53, v0=600) After retessellation of defect 3 (v0=600), euler #=-106 (125291,370510,245113) : difference with theory (-102) = 4 CORRECTING DEFECT 4 (vertices=805, convex hull=557, v0=1187) L defect detected... After retessellation of defect 4 (v0=1187), euler #=-104 (125433,371248,245711) : difference with theory (-101) = 3 CORRECTING DEFECT 5 (vertices=338, convex hull=245, v0=5539) After retessellation of defect 5 (v0=5539), euler #=-101 (125492,371553,245960) : difference with theory (-100) = 1 CORRECTING DEFECT 6 (vertices=123, convex hull=84, v0=6150) After retessellation of defect 6 (v0=6150), euler #=-100 (125525,371689,246064) : difference with theory (-99) = 1 CORRECTING DEFECT 7 (vertices=103, convex hull=96, v0=6408) After retessellation of defect 7 (v0=6408), euler #=-99 (125568,371859,246192) : difference with theory (-98) = 1 CORRECTING DEFECT 8 (vertices=85, convex hull=108, v0=7633) After retessellation of defect 8 (v0=7633), euler #=-98 (125584,371955,246273) : difference with theory (-97) = 1 CORRECTING DEFECT 9 (vertices=41, convex hull=101, v0=8130) After retessellation of defect 9 (v0=8130), euler #=-97 (125610,372071,246364) : difference with theory (-96) = 1 CORRECTING DEFECT 10 (vertices=34, convex hull=76, v0=8262) After retessellation of defect 10 (v0=8262), euler #=-96 (125619,372129,246414) : difference with theory (-95) = 1 CORRECTING DEFECT 11 (vertices=599, convex hull=340, v0=10567) After retessellation of defect 11 (v0=10567), euler #=-94 (125853,373042,247095) : difference with theory (-94) = 0 CORRECTING DEFECT 12 (vertices=225, convex hull=164, v0=10571) After retessellation of defect 12 (v0=10571), euler #=-93 (125967,373462,247402) : difference with theory (-93) = 0 CORRECTING DEFECT 13 (vertices=401, convex hull=75, v0=11189) After retessellation of defect 13 (v0=11189), euler #=-92 (126000,373595,247503) : difference with theory (-92) = 0 CORRECTING DEFECT 14 (vertices=111, convex hull=90, v0=13953) After retessellation of defect 14 (v0=13953), euler #=-91 (126032,373732,247609) : difference with theory (-91) = 0 CORRECTING DEFECT 15 (vertices=71, convex hull=90, v0=15117) After retessellation of defect 15 (v0=15117), euler #=-90 (126049,373822,247683) : difference with theory (-90) = 0 CORRECTING DEFECT 16 (vertices=15, convex hull=34, v0=15361) After retessellation of defect 16 (v0=15361), euler #=-89 (126052,373842,247701) : difference with theory (-89) = 0 CORRECTING DEFECT 17 (vertices=106, convex hull=99, v0=16392) After retessellation of defect 17 (v0=16392), euler #=-88 (126105,374044,247851) : difference with theory (-88) = 0 CORRECTING DEFECT 18 (vertices=15, convex hull=17, v0=18878) After retessellation of defect 18 (v0=18878), euler #=-87 (126106,374052,247859) : difference with theory (-87) = 0 CORRECTING DEFECT 19 (vertices=67, convex hull=84, v0=20010) After retessellation of defect 19 (v0=20010), euler #=-86 (126138,374181,247957) : difference with theory (-86) = 0 CORRECTING DEFECT 20 (vertices=21, convex hull=57, v0=21225) After retessellation of defect 20 (v0=21225), euler #=-85 (126149,374236,248002) : difference with theory (-85) = 0 CORRECTING DEFECT 21 (vertices=86, convex hull=55, v0=21526) After retessellation of defect 21 (v0=21526), euler #=-84 (126158,374287,248045) : difference with theory (-84) = 0 CORRECTING DEFECT 22 (vertices=5, convex hull=18, v0=22310) After retessellation of defect 22 (v0=22310), euler #=-83 (126158,374291,248050) : difference with theory (-83) = 0 CORRECTING DEFECT 23 (vertices=96, convex hull=124, v0=23786) After retessellation of defect 23 (v0=23786), euler #=-83 (126198,374483,248202) : difference with theory (-82) = 1 CORRECTING DEFECT 24 (vertices=126, convex hull=127, v0=24075) After retessellation of defect 24 (v0=24075), euler #=-82 (126268,374752,248402) : difference with theory (-81) = 1 CORRECTING DEFECT 25 (vertices=51, convex hull=116, v0=24324) After retessellation of defect 25 (v0=24324), euler #=-81 (126298,374888,248509) : difference with theory (-80) = 1 CORRECTING DEFECT 26 (vertices=153, convex hull=181, v0=25006) After retessellation of defect 26 (v0=25006), euler #=-80 (126390,375251,248781) : difference with theory (-79) = 1 CORRECTING DEFECT 27 (vertices=185, convex hull=134, v0=25129) After retessellation of defect 27 (v0=25129), euler #=-80 (126469,375566,249017) : difference with theory (-78) = 2 CORRECTING DEFECT 28 (vertices=31, convex hull=73, v0=28119) After retessellation of defect 28 (v0=28119), euler #=-79 (126490,375659,249090) : difference with theory (-77) = 2 CORRECTING DEFECT 29 (vertices=94, convex hull=113, v0=29627) After retessellation of defect 29 (v0=29627), euler #=-78 (126533,375839,249228) : difference with theory (-76) = 2 CORRECTING DEFECT 30 (vertices=84, convex hull=72, v0=29822) After retessellation of defect 30 (v0=29822), euler #=-77 (126556,375937,249304) : difference with theory (-75) = 2 CORRECTING DEFECT 31 (vertices=2168, convex hull=564, v0=30155) XL defect detected... After retessellation of defect 31 (v0=30155), euler #=-75 (126870,377169,250224) : difference with theory (-74) = 1 CORRECTING DEFECT 32 (vertices=62, convex hull=57, v0=33561) After retessellation of defect 32 (v0=33561), euler #=-74 (126877,377214,250263) : difference with theory (-73) = 1 CORRECTING DEFECT 33 (vertices=130, convex hull=51, v0=33633) After retessellation of defect 33 (v0=33633), euler #=-73 (126900,377304,250331) : difference with theory (-72) = 1 CORRECTING DEFECT 34 (vertices=29, convex hull=38, v0=36016) After retessellation of defect 34 (v0=36016), euler #=-72 (126904,377330,250354) : difference with theory (-71) = 1 CORRECTING DEFECT 35 (vertices=69, convex hull=97, v0=36148) After retessellation of defect 35 (v0=36148), euler #=-71 (126934,377457,250452) : difference with theory (-70) = 1 CORRECTING DEFECT 36 (vertices=23, convex hull=46, v0=36203) After retessellation of defect 36 (v0=36203), euler #=-70 (126945,377506,250491) : difference with theory (-69) = 1 CORRECTING DEFECT 37 (vertices=34, convex hull=26, v0=38980) After retessellation of defect 37 (v0=38980), euler #=-69 (126948,377524,250507) : difference with theory (-68) = 1 CORRECTING DEFECT 38 (vertices=38, convex hull=77, v0=45209) After retessellation of defect 38 (v0=45209), euler #=-68 (126972,377629,250589) : difference with theory (-67) = 1 CORRECTING DEFECT 39 (vertices=18, convex hull=36, v0=46065) After retessellation of defect 39 (v0=46065), euler #=-67 (126972,377640,250601) : difference with theory (-66) = 1 CORRECTING DEFECT 40 (vertices=93, convex hull=95, v0=46212) After retessellation of defect 40 (v0=46212), euler #=-66 (127018,377819,250735) : difference with theory (-65) = 1 CORRECTING DEFECT 41 (vertices=40, convex hull=31, v0=48255) After retessellation of defect 41 (v0=48255), euler #=-65 (127021,377837,250751) : difference with theory (-64) = 1 CORRECTING DEFECT 42 (vertices=517, convex hull=247, v0=48285) After retessellation of defect 42 (v0=48285), euler #=-65 (127277,378739,251397) : difference with theory (-63) = 2 CORRECTING DEFECT 43 (vertices=86, convex hull=127, v0=48373) After retessellation of defect 43 (v0=48373), euler #=-64 (127331,378956,251561) : difference with theory (-62) = 2 CORRECTING DEFECT 44 (vertices=113, convex hull=121, v0=48476) After retessellation of defect 44 (v0=48476), euler #=-63 (127368,379122,251691) : difference with theory (-61) = 2 CORRECTING DEFECT 45 (vertices=68, convex hull=107, v0=48805) After retessellation of defect 45 (v0=48805), euler #=-62 (127411,379298,251825) : difference with theory (-60) = 2 CORRECTING DEFECT 46 (vertices=52, convex hull=71, v0=50418) After retessellation of defect 46 (v0=50418), euler #=-61 (127437,379402,251904) : difference with theory (-59) = 2 CORRECTING DEFECT 47 (vertices=95, convex hull=109, v0=52119) After retessellation of defect 47 (v0=52119), euler #=-60 (127486,379598,252052) : difference with theory (-58) = 2 CORRECTING DEFECT 48 (vertices=13, convex hull=30, v0=54176) After retessellation of defect 48 (v0=54176), euler #=-59 (127487,379611,252065) : difference with theory (-57) = 2 CORRECTING DEFECT 49 (vertices=58, convex hull=28, v0=54483) After retessellation of defect 49 (v0=54483), euler #=-58 (127493,379639,252088) : difference with theory (-56) = 2 CORRECTING DEFECT 50 (vertices=29, convex hull=39, v0=55697) After retessellation of defect 50 (v0=55697), euler #=-57 (127500,379674,252117) : difference with theory (-55) = 2 CORRECTING DEFECT 51 (vertices=49, convex hull=63, v0=55973) After retessellation of defect 51 (v0=55973), euler #=-56 (127509,379727,252162) : difference with theory (-54) = 2 CORRECTING DEFECT 52 (vertices=111, convex hull=120, v0=55995) After retessellation of defect 52 (v0=55995), euler #=-55 (127525,379825,252245) : difference with theory (-53) = 2 CORRECTING DEFECT 53 (vertices=48, convex hull=30, v0=58016) After retessellation of defect 53 (v0=58016), euler #=-54 (127529,379847,252264) : difference with theory (-52) = 2 CORRECTING DEFECT 54 (vertices=32, convex hull=26, v0=60670) After retessellation of defect 54 (v0=60670), euler #=-53 (127530,379859,252276) : difference with theory (-51) = 2 CORRECTING DEFECT 55 (vertices=65, convex hull=69, v0=63467) After retessellation of defect 55 (v0=63467), euler #=-52 (127555,379959,252352) : difference with theory (-50) = 2 CORRECTING DEFECT 56 (vertices=103, convex hull=51, v0=63725) After retessellation of defect 56 (v0=63725), euler #=-51 (127564,380004,252389) : difference with theory (-49) = 2 CORRECTING DEFECT 57 (vertices=26, convex hull=42, v0=64960) After retessellation of defect 57 (v0=64960), euler #=-50 (127570,380032,252412) : difference with theory (-48) = 2 CORRECTING DEFECT 58 (vertices=83, convex hull=45, v0=65243) After retessellation of defect 58 (v0=65243), euler #=-49 (127577,380073,252447) : difference with theory (-47) = 2 CORRECTING DEFECT 59 (vertices=122, convex hull=32, v0=65841) After retessellation of defect 59 (v0=65841), euler #=-48 (127588,380117,252481) : difference with theory (-46) = 2 CORRECTING DEFECT 60 (vertices=1215, convex hull=306, v0=66443) L defect detected... After retessellation of defect 60 (v0=66443), euler #=-47 (127787,380881,253047) : difference with theory (-45) = 2 CORRECTING DEFECT 61 (vertices=23, convex hull=58, v0=66630) After retessellation of defect 61 (v0=66630), euler #=-46 (127798,380936,253092) : difference with theory (-44) = 2 CORRECTING DEFECT 62 (vertices=62, convex hull=76, v0=66851) After retessellation of defect 62 (v0=66851), euler #=-45 (127840,381091,253206) : difference with theory (-43) = 2 CORRECTING DEFECT 63 (vertices=15, convex hull=19, v0=67069) After retessellation of defect 63 (v0=67069), euler #=-44 (127841,381098,253213) : difference with theory (-42) = 2 CORRECTING DEFECT 64 (vertices=4032, convex hull=1514, v0=71524) XL defect detected... After retessellation of defect 64 (v0=71524), euler #=-40 (128215,383019,254764) : difference with theory (-41) = -1 CORRECTING DEFECT 65 (vertices=62, convex hull=128, v0=73354) After retessellation of defect 65 (v0=73354), euler #=-39 (128261,383210,254910) : difference with theory (-40) = -1 CORRECTING DEFECT 66 (vertices=6, convex hull=15, v0=79212) After retessellation of defect 66 (v0=79212), euler #=-38 (128262,383219,254919) : difference with theory (-39) = -1 CORRECTING DEFECT 67 (vertices=29, convex hull=31, v0=82932) After retessellation of defect 67 (v0=82932), euler #=-37 (128266,383241,254938) : difference with theory (-38) = -1 CORRECTING DEFECT 68 (vertices=228, convex hull=188, v0=89101) After retessellation of defect 68 (v0=89101), euler #=-35 (128385,383693,255273) : difference with theory (-37) = -2 CORRECTING DEFECT 69 (vertices=12, convex hull=24, v0=92689) After retessellation of defect 69 (v0=92689), euler #=-34 (128387,383707,255286) : difference with theory (-36) = -2 CORRECTING DEFECT 70 (vertices=62, convex hull=84, v0=92787) After retessellation of defect 70 (v0=92787), euler #=-33 (128418,383834,255383) : difference with theory (-35) = -2 CORRECTING DEFECT 71 (vertices=19, convex hull=22, v0=94049) After retessellation of defect 71 (v0=94049), euler #=-32 (128419,383842,255391) : difference with theory (-34) = -2 CORRECTING DEFECT 72 (vertices=766, convex hull=302, v0=94066) After retessellation of defect 72 (v0=94066), euler #=-31 (128582,384486,255873) : difference with theory (-33) = -2 CORRECTING DEFECT 73 (vertices=48, convex hull=36, v0=94920) After retessellation of defect 73 (v0=94920), euler #=-30 (128588,384514,255896) : difference with theory (-32) = -2 CORRECTING DEFECT 74 (vertices=45, convex hull=56, v0=95067) After retessellation of defect 74 (v0=95067), euler #=-29 (128597,384563,255937) : difference with theory (-31) = -2 CORRECTING DEFECT 75 (vertices=27, convex hull=61, v0=97120) After retessellation of defect 75 (v0=97120), euler #=-28 (128614,384637,255995) : difference with theory (-30) = -2 CORRECTING DEFECT 76 (vertices=30, convex hull=39, v0=100711) After retessellation of defect 76 (v0=100711), euler #=-27 (128617,384657,256013) : difference with theory (-29) = -2 CORRECTING DEFECT 77 (vertices=67, convex hull=25, v0=101808) After retessellation of defect 77 (v0=101808), euler #=-26 (128621,384677,256030) : difference with theory (-28) = -2 CORRECTING DEFECT 78 (vertices=38, convex hull=43, v0=102645) After retessellation of defect 78 (v0=102645), euler #=-25 (128628,384714,256061) : difference with theory (-27) = -2 CORRECTING DEFECT 79 (vertices=61, convex hull=101, v0=102790) After retessellation of defect 79 (v0=102790), euler #=-24 (128666,384870,256180) : difference with theory (-26) = -2 CORRECTING DEFECT 80 (vertices=621, convex hull=306, v0=108281) After retessellation of defect 80 (v0=108281), euler #=-24 (128799,385425,256602) : difference with theory (-25) = -1 CORRECTING DEFECT 81 (vertices=337, convex hull=118, v0=108330) After retessellation of defect 81 (v0=108330), euler #=-23 (128842,385607,256742) : difference with theory (-24) = -1 CORRECTING DEFECT 82 (vertices=193, convex hull=38, v0=108582) After retessellation of defect 82 (v0=108582), euler #=-22 (128858,385669,256789) : difference with theory (-23) = -1 CORRECTING DEFECT 83 (vertices=22, convex hull=48, v0=112052) After retessellation of defect 83 (v0=112052), euler #=-21 (128863,385703,256819) : difference with theory (-22) = -1 CORRECTING DEFECT 84 (vertices=179, convex hull=48, v0=114362) After retessellation of defect 84 (v0=114362), euler #=-20 (128878,385766,256868) : difference with theory (-21) = -1 CORRECTING DEFECT 85 (vertices=32, convex hull=43, v0=116208) After retessellation of defect 85 (v0=116208), euler #=-19 (128879,385783,256885) : difference with theory (-20) = -1 CORRECTING DEFECT 86 (vertices=92, convex hull=51, v0=117716) After retessellation of defect 86 (v0=117716), euler #=-18 (128894,385851,256939) : difference with theory (-19) = -1 CORRECTING DEFECT 87 (vertices=97, convex hull=113, v0=118086) After retessellation of defect 87 (v0=118086), euler #=-17 (128958,386096,257121) : difference with theory (-18) = -1 CORRECTING DEFECT 88 (vertices=464, convex hull=298, v0=121139) After retessellation of defect 88 (v0=121139), euler #=-16 (129070,386593,257507) : difference with theory (-17) = -1 CORRECTING DEFECT 89 (vertices=283, convex hull=62, v0=124090) After retessellation of defect 89 (v0=124090), euler #=-15 (129086,386674,257573) : difference with theory (-16) = -1 CORRECTING DEFECT 90 (vertices=805, convex hull=286, v0=124779) After retessellation of defect 90 (v0=124779), euler #=-14 (129271,387380,258095) : difference with theory (-15) = -1 CORRECTING DEFECT 91 (vertices=73, convex hull=75, v0=126820) After retessellation of defect 91 (v0=126820), euler #=-13 (129308,387523,258202) : difference with theory (-14) = -1 CORRECTING DEFECT 92 (vertices=104, convex hull=100, v0=130295) After retessellation of defect 92 (v0=130295), euler #=-13 (129357,387719,258349) : difference with theory (-13) = 0 CORRECTING DEFECT 93 (vertices=57, convex hull=76, v0=131631) After retessellation of defect 93 (v0=131631), euler #=-12 (129396,387870,258462) : difference with theory (-12) = 0 CORRECTING DEFECT 94 (vertices=8, convex hull=23, v0=132792) After retessellation of defect 94 (v0=132792), euler #=-11 (129397,387883,258475) : difference with theory (-11) = 0 CORRECTING DEFECT 95 (vertices=37, convex hull=70, v0=133803) After retessellation of defect 95 (v0=133803), euler #=-10 (129409,387951,258532) : difference with theory (-10) = 0 CORRECTING DEFECT 96 (vertices=82, convex hull=118, v0=134505) After retessellation of defect 96 (v0=134505), euler #=-9 (129451,388121,258661) : difference with theory (-9) = 0 CORRECTING DEFECT 97 (vertices=31, convex hull=14, v0=138199) After retessellation of defect 97 (v0=138199), euler #=-8 (129451,388124,258665) : difference with theory (-8) = 0 CORRECTING DEFECT 98 (vertices=87, convex hull=38, v0=138876) After retessellation of defect 98 (v0=138876), euler #=-7 (129456,388153,258690) : difference with theory (-7) = 0 CORRECTING DEFECT 99 (vertices=43, convex hull=90, v0=139211) After retessellation of defect 99 (v0=139211), euler #=-6 (129484,388273,258783) : difference with theory (-6) = 0 CORRECTING DEFECT 100 (vertices=28, convex hull=28, v0=139881) After retessellation of defect 100 (v0=139881), euler #=-5 (129487,388294,258802) : difference with theory (-5) = 0 CORRECTING DEFECT 101 (vertices=17, convex hull=58, v0=141619) After retessellation of defect 101 (v0=141619), euler #=-4 (129495,388337,258838) : difference with theory (-4) = 0 CORRECTING DEFECT 102 (vertices=6, convex hull=18, v0=142438) After retessellation of defect 102 (v0=142438), euler #=-3 (129495,388342,258844) : difference with theory (-3) = 0 CORRECTING DEFECT 103 (vertices=48, convex hull=43, v0=143247) After retessellation of defect 103 (v0=143247), euler #=-2 (129498,388365,258865) : difference with theory (-2) = 0 CORRECTING DEFECT 104 (vertices=48, convex hull=75, v0=143358) After retessellation of defect 104 (v0=143358), euler #=-1 (129510,388429,258918) : difference with theory (-1) = 0 CORRECTING DEFECT 105 (vertices=99, convex hull=31, v0=144159) After retessellation of defect 105 (v0=144159), euler #=0 (129515,388453,258938) : difference with theory (0) = 0 CORRECTING DEFECT 106 (vertices=223, convex hull=155, v0=144210) After retessellation of defect 106 (v0=144210), euler #=1 (129551,388631,259081) : difference with theory (1) = 0 CORRECTING DEFECT 107 (vertices=125, convex hull=48, v0=144653) After retessellation of defect 107 (v0=144653), euler #=2 (129560,388674,259116) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.36 (0.04-->27.30) (max @ vno 69448 --> 92233) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.36 (0.04-->27.30) (max @ vno 69448 --> 92233) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 295 mutations (32.9%), 602 crossovers (67.1%), 2096 vertices were eliminated building final representation... 15864 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=129560, nf=259116, ne=388674, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 364.5 minutes 0 defective edges removing intersecting faces 000: 1754 intersecting 001: 106 intersecting 002: 64 intersecting expanding nbhd size to 2 003: 67 intersecting 004: 62 intersecting 005: 59 intersecting expanding nbhd size to 3 006: 64 intersecting 007: 54 intersecting 008: 43 intersecting 009: 33 intersecting expanding nbhd size to 4 010: 50 intersecting 011: 31 intersecting 012: 15 intersecting 013: 14 intersecting 014: 10 intersecting expanding nbhd size to 5 015: 12 intersecting 016: 9 intersecting mris_fix_topology utimesec 10936.256436 mris_fix_topology stimesec 3.080531 mris_fix_topology ru_maxrss 613132 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 88702 mris_fix_topology ru_majflt 3 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 20592 mris_fix_topology ru_oublock 13344 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 258 mris_fix_topology ru_nivcsw 1096571 FSRUNTIME@ mris_fix_topology rh 6.0743 hours 1 threads PIDs (20548 20551) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 131248 - 393738 + 262492 = 2 --> 0 holes F =2V-4: 262492 = 262496-4 (0) 2E=3F: 787476 = 787476 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 129560 - 388674 + 259116 = 2 --> 0 holes F =2V-4: 259116 = 259120-4 (0) 2E=3F: 777348 = 777348 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 1267 intersecting 001: 333 intersecting 002: 225 intersecting 003: 196 intersecting 004: 155 intersecting 005: 130 intersecting 006: 107 intersecting expanding nbhd size to 2 007: 113 intersecting 008: 83 intersecting 009: 58 intersecting 010: 47 intersecting 011: 37 intersecting 012: 28 intersecting 013: 12 intersecting 014: 4 intersecting 015: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 485 intersecting 001: 95 intersecting 002: 73 intersecting 003: 67 intersecting expanding nbhd size to 2 004: 67 intersecting 005: 56 intersecting expanding nbhd size to 3 006: 60 intersecting 007: 51 intersecting 008: 45 intersecting 009: 35 intersecting expanding nbhd size to 4 010: 38 intersecting 011: 34 intersecting expanding nbhd size to 5 012: 42 intersecting 013: 17 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 29 03:45:45 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 29 03:45:45 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 rh Waiting for PID 25638 of (25638 25641) to complete... Waiting for PID 25641 of (25638 25641) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... 23908 bright wm thresholded. 4134 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig... computing class statistics... border white: 256030 voxels (1.53%) border gray 340019 voxels (2.03%) WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0] GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70) setting MAX_BORDER_WHITE to 104.9 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 40.8 (was 40) setting MAX_GRAY to 87.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.29 (0.01-->11.21) (max @ vno 57431 --> 125716) face area 0.28 +- 0.19 (0.00-->16.27) mean absolute distance = 0.75 +- 0.96 3886 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=96+-8.7, GM=63+-8.7 mean inside = 89.3, mean outside = 71.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=75.7, 527 (527) missing vertices, mean dist 0.3 [0.7 (%33.2)->0.8 (%66.8))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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 0.93 +- 0.33 (0.04-->11.60) (max @ vno 57431 --> 125716) face area 0.28 +- 0.18 (0.00-->14.20) mean absolute distance = 0.38 +- 0.68 3992 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3414600.5, rms=10.249 001: dt: 0.5000, sse=2057774.0, rms=7.684 (25.031%) 002: dt: 0.5000, sse=1523707.0, rms=6.203 (19.269%) 003: dt: 0.5000, sse=1247211.4, rms=5.289 (14.742%) 004: dt: 0.5000, sse=1112542.5, rms=4.771 (9.780%) 005: dt: 0.5000, sse=1042551.9, rms=4.465 (6.416%) 006: dt: 0.5000, sse=1006678.9, rms=4.297 (3.760%) 007: dt: 0.5000, sse=978989.6, rms=4.181 (2.710%) 008: dt: 0.5000, sse=968210.2, rms=4.130 (1.205%) 009: dt: 0.5000, sse=965118.4, rms=4.072 (1.412%) rms = 4.04, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=955012.9, rms=4.040 (0.795%) 011: dt: 0.2500, sse=786997.6, rms=3.052 (24.442%) 012: dt: 0.2500, sse=761400.9, rms=2.819 (7.654%) 013: dt: 0.2500, sse=744242.4, rms=2.755 (2.248%) rms = 2.72, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=744245.8, rms=2.724 (1.141%) 015: dt: 0.1250, sse=729110.2, rms=2.656 (2.492%) rms = 2.64, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=728576.2, rms=2.641 (0.572%) positioning took 3.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=78.2, 524 (141) missing vertices, mean dist -0.2 [0.4 (%66.3)->0.3 (%33.7))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 0.93 +- 0.32 (0.04-->11.66) (max @ vno 57431 --> 125716) face area 0.36 +- 0.24 (0.00-->18.43) mean absolute distance = 0.29 +- 0.50 3219 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1170418.9, rms=4.311 017: dt: 0.5000, sse=1021326.6, rms=3.351 (22.255%) rms = 3.51, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=894051.3, rms=2.739 (18.267%) 019: dt: 0.2500, sse=877563.2, rms=2.426 (11.433%) 020: dt: 0.2500, sse=847438.1, rms=2.322 (4.300%) rms = 2.29, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=847790.2, rms=2.289 (1.409%) 022: dt: 0.1250, sse=828879.2, rms=2.215 (3.241%) rms = 2.20, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=826171.1, rms=2.196 (0.837%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.5, 626 (99) missing vertices, mean dist -0.1 [0.3 (%59.2)->0.3 (%40.8))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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 +- 0.32 (0.06-->11.60) (max @ vno 57431 --> 125716) face area 0.35 +- 0.24 (0.00-->18.33) mean absolute distance = 0.28 +- 0.43 3470 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=903947.8, rms=2.864 rms = 2.92, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=841668.8, rms=2.376 (17.031%) 025: dt: 0.2500, sse=812065.6, rms=2.093 (11.907%) rms = 2.06, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=806732.8, rms=2.060 (1.568%) 027: dt: 0.1250, sse=794903.2, rms=1.970 (4.369%) rms = 1.95, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=803366.7, rms=1.948 (1.146%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.1, 662 (84) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=821219.4, rms=2.149 rms = 2.22, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=779452.2, rms=1.825 (15.046%) 030: dt: 0.2500, sse=772902.9, rms=1.655 (9.312%) rms = 1.68, time step reduction 2 of 3 to 0.125... rms = 1.63, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=762235.4, rms=1.632 (1.440%) positioning took 0.9 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6516 vertices erasing segment 0 (vno[0] = 31021) erasing segment 1 (vno[0] = 34449) erasing segment 2 (vno[0] = 36478) erasing segment 3 (vno[0] = 37545) erasing segment 5 (vno[0] = 81973) erasing segment 6 (vno[0] = 82914) erasing segment 7 (vno[0] = 88867) erasing segment 8 (vno[0] = 94720) erasing segment 9 (vno[0] = 96228) erasing segment 10 (vno[0] = 105551) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.area vertex spacing 0.92 +- 0.32 (0.02-->11.65) (max @ vno 57431 --> 125716) face area 0.35 +- 0.23 (0.00-->18.31) refinement took 9.4 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050418 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... 23908 bright wm thresholded. 4134 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig... computing class statistics... border white: 256030 voxels (1.53%) border gray 340019 voxels (2.03%) WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0] GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70) setting MAX_BORDER_WHITE to 104.9 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 40.8 (was 40) setting MAX_GRAY to 87.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.26 (0.02-->9.64) (max @ vno 69448 --> 92233) face area 0.28 +- 0.16 (0.00-->13.62) mean absolute distance = 0.72 +- 0.88 3795 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=96+-9.6, GM=63+-9.6 mean inside = 89.8, mean outside = 71.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=76.0, 224 (224) missing vertices, mean dist 0.3 [0.6 (%33.0)->0.8 (%67.0))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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 0.93 +- 0.30 (0.06-->9.84) (max @ vno 69448 --> 92233) face area 0.28 +- 0.16 (0.00-->10.88) mean absolute distance = 0.36 +- 0.63 3486 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3459371.0, rms=10.663 001: dt: 0.5000, sse=2028926.6, rms=7.805 (26.802%) 002: dt: 0.5000, sse=1434236.0, rms=6.094 (21.914%) 003: dt: 0.5000, sse=1148175.0, rms=5.059 (16.998%) 004: dt: 0.5000, sse=1015404.9, rms=4.479 (11.456%) 005: dt: 0.5000, sse=947584.1, rms=4.175 (6.787%) 006: dt: 0.5000, sse=916542.9, rms=4.012 (3.896%) 007: dt: 0.5000, sse=911968.5, rms=3.924 (2.208%) 008: dt: 0.5000, sse=887991.9, rms=3.860 (1.634%) rms = 3.83, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=883283.9, rms=3.827 (0.835%) 010: dt: 0.2500, sse=718156.4, rms=2.754 (28.051%) 011: dt: 0.2500, sse=687600.1, rms=2.480 (9.925%) 012: dt: 0.2500, sse=677312.6, rms=2.419 (2.490%) rms = 2.38, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=676274.1, rms=2.383 (1.474%) 014: dt: 0.1250, sse=663993.9, rms=2.309 (3.105%) rms = 2.30, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=662009.2, rms=2.296 (0.561%) positioning took 2.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=78.7, 272 (43) missing vertices, mean dist -0.2 [0.4 (%67.3)->0.3 (%32.7))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 +- 0.30 (0.06-->9.87) (max @ vno 69448 --> 92233) face area 0.36 +- 0.20 (0.00-->14.46) mean absolute distance = 0.29 +- 0.47 3436 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1149162.4, rms=4.365 016: dt: 0.5000, sse=942952.4, rms=3.164 (27.509%) rms = 3.35, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=835394.2, rms=2.488 (21.381%) 018: dt: 0.2500, sse=794215.7, rms=2.141 (13.945%) 019: dt: 0.2500, sse=782259.4, rms=2.008 (6.199%) rms = 1.98, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=776670.8, rms=1.975 (1.627%) 021: dt: 0.1250, sse=768080.9, rms=1.904 (3.625%) rms = 1.89, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=766807.1, rms=1.891 (0.648%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=80.2, 364 (26) missing vertices, mean dist -0.1 [0.3 (%59.6)->0.3 (%40.4))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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 +- 0.29 (0.05-->9.82) (max @ vno 69448 --> 92233) face area 0.35 +- 0.20 (0.00-->14.35) mean absolute distance = 0.27 +- 0.42 3074 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=842306.8, rms=2.655 rms = 2.74, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=778524.1, rms=2.105 (20.714%) 024: dt: 0.2500, sse=755053.1, rms=1.781 (15.396%) rms = 1.74, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=752048.2, rms=1.736 (2.500%) 026: dt: 0.1250, sse=739136.0, rms=1.667 (3.992%) rms = 1.66, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=736909.9, rms=1.658 (0.547%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=80.8, 418 (17) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=750256.2, rms=1.867 rms = 1.95, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=717741.4, rms=1.493 (20.041%) 029: dt: 0.2500, sse=707741.9, rms=1.300 (12.945%) rms = 1.31, time step reduction 2 of 3 to 0.125... rms = 1.29, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=703833.9, rms=1.285 (1.142%) positioning took 0.8 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6313 vertices erasing segment 0 (vno[0] = 31921) erasing segment 2 (vno[0] = 82688) erasing segment 3 (vno[0] = 86120) erasing segment 4 (vno[0] = 87128) erasing segment 5 (vno[0] = 93751) erasing segment 6 (vno[0] = 95923) erasing segment 7 (vno[0] = 96633) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.area vertex spacing 0.91 +- 0.30 (0.02-->9.81) (max @ vno 69448 --> 92233) face area 0.35 +- 0.20 (0.00-->14.27) refinement took 9.2 minutes PIDs (25638 25641) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 29 03:55:09 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 29 03:55:09 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 26001 of (26001 26004) to complete... Waiting for PID 26004 of (26001 26004) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (26001 26004) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 29 03:55:19 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 29 03:55:19 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 26043 of (26043 26046) to complete... Waiting for PID 26046 of (26043 26046) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.2 mm, total surface area = 82010 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.201 (target=0.015) step 005: RMS=0.145 (target=0.015) step 010: RMS=0.119 (target=0.015) step 015: RMS=0.101 (target=0.015) step 020: RMS=0.088 (target=0.015) step 025: RMS=0.076 (target=0.015) step 030: RMS=0.065 (target=0.015) step 035: RMS=0.058 (target=0.015) step 040: RMS=0.052 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.041 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. inflation took 1.1 minutes mris_inflate utimesec 32.000135 mris_inflate stimesec 0.073988 mris_inflate ru_maxrss 170560 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22772 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 12280 mris_inflate ru_oublock 10288 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 293 mris_inflate ru_nivcsw 3423 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.7 mm, total surface area = 80296 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.198 (target=0.015) step 005: RMS=0.142 (target=0.015) step 010: RMS=0.116 (target=0.015) step 015: RMS=0.098 (target=0.015) step 020: RMS=0.086 (target=0.015) step 025: RMS=0.075 (target=0.015) step 030: RMS=0.065 (target=0.015) step 035: RMS=0.060 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.046 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 31.209255 mris_inflate stimesec 0.067989 mris_inflate ru_maxrss 167968 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22126 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10152 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 216 mris_inflate ru_nivcsw 3206 PIDs (26043 26046) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 29 03:56:23 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun Oct 29 03:56:23 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf mris_curvature -w rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 26163 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26166 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26169 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26172 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26175 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26178 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26181 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26184 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26187 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26190 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26193 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... Waiting for PID 26196 of (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 31.877*4pi (400.582) --> -31 handles ICI = 255.1, FI = 2114.2, variation=34772.835 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 166 vertices thresholded to be in k1 ~ [-0.47 1.68], k2 ~ [-0.30 0.16] total integrated curvature = -0.095*4pi (-1.193) --> 1 handles ICI = 1.4, FI = 8.2, variation=153.681 149 vertices thresholded to be in [-0.12 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 109 vertices thresholded to be in [-0.18 0.61] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.024 done. mris_curvature -w rh.white.preaparc total integrated curvature = 29.682*4pi (372.993) --> -29 handles ICI = 241.7, FI = 1990.7, variation=32771.932 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 171 vertices thresholded to be in k1 ~ [-0.64 1.70], k2 ~ [-0.34 0.19] total integrated curvature = 0.110*4pi (1.376) --> 1 handles ICI = 1.3, FI = 9.9, variation=166.955 154 vertices thresholded to be in [-0.12 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = -0.000, std = 0.003 97 vertices thresholded to be in [-0.25 0.49] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.025 done. PIDs (26163 26166 26169 26172 26175 26178 26181 26184 26187 26190 26193 26196) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 29 03:59:09 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050418 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 [ 0050418/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 [ 278 ] Gb_filter = 0 WARN: S lookup min: -1.325662 WARN: S explicit min: 0.000000 vertex = 684 #----------------------------------------- #@# Curvature Stats rh Sun Oct 29 03:59:13 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050418 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 [ 0050418/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 [ 253 ] Gb_filter = 0 WARN: S lookup min: -0.038302 WARN: S explicit min: 0.000000 vertex = 1 #-------------------------------------------- #@# Sphere lh Sun Oct 29 03:59:16 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 29 03:59:16 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 26369 of (26369 26372) to complete... Waiting for PID 26372 of (26369 26372) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.299... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %22.35 pass 1: epoch 2 of 3 starting distance error %22.26 unfolding complete - removing small folds... starting distance error %21.82 removing remaining folds... final distance error %21.87 MRISunfold() return, current seed 1234 -01: dt=0.0000, 471 negative triangles 381: dt=0.9900, 471 negative triangles 382: dt=0.9900, 206 negative triangles 383: dt=0.9900, 140 negative triangles 384: dt=0.9900, 130 negative triangles 385: dt=0.9900, 108 negative triangles 386: dt=0.9900, 107 negative triangles 387: dt=0.9900, 95 negative triangles 388: dt=0.9900, 80 negative triangles 389: dt=0.9900, 87 negative triangles 390: dt=0.9900, 79 negative triangles 391: dt=0.9900, 66 negative triangles 392: dt=0.9900, 71 negative triangles 393: dt=0.9900, 71 negative triangles 394: dt=0.9900, 67 negative triangles 395: dt=0.9900, 67 negative triangles 396: dt=0.9900, 67 negative triangles 397: dt=0.9900, 61 negative triangles 398: dt=0.9900, 61 negative triangles 399: dt=0.9900, 60 negative triangles 400: dt=0.9900, 55 negative triangles 401: dt=0.9900, 52 negative triangles 402: dt=0.9900, 48 negative triangles 403: dt=0.9900, 54 negative triangles 404: dt=0.9900, 48 negative triangles 405: dt=0.9900, 50 negative triangles 406: dt=0.9900, 54 negative triangles 407: dt=0.9900, 47 negative triangles 408: dt=0.9900, 48 negative triangles 409: dt=0.9900, 45 negative triangles 410: dt=0.9900, 44 negative triangles 411: dt=0.9900, 49 negative triangles 412: dt=0.9900, 51 negative triangles 413: dt=0.9900, 44 negative triangles 414: dt=0.9900, 44 negative triangles 415: dt=0.9900, 42 negative triangles 416: dt=0.9900, 45 negative triangles 417: dt=0.9900, 46 negative triangles 418: dt=0.9900, 36 negative triangles 419: dt=0.9900, 43 negative triangles 420: dt=0.9900, 42 negative triangles 421: dt=0.9900, 36 negative triangles 422: dt=0.9900, 38 negative triangles 423: dt=0.9900, 39 negative triangles 424: dt=0.9900, 37 negative triangles 425: dt=0.9900, 43 negative triangles 426: dt=0.9900, 41 negative triangles 427: dt=0.9900, 38 negative triangles 428: dt=0.9405, 38 negative triangles 429: dt=0.9405, 33 negative triangles 430: dt=0.9405, 40 negative triangles 431: dt=0.9405, 37 negative triangles 432: dt=0.9405, 32 negative triangles 433: dt=0.9405, 32 negative triangles 434: dt=0.9405, 32 negative triangles 435: dt=0.9405, 29 negative triangles 436: dt=0.9405, 27 negative triangles 437: dt=0.9405, 30 negative triangles 438: dt=0.9405, 27 negative triangles 439: dt=0.9405, 29 negative triangles 440: dt=0.9405, 29 negative triangles 441: dt=0.9405, 26 negative triangles 442: dt=0.9405, 23 negative triangles 443: dt=0.9405, 22 negative triangles 444: dt=0.9405, 22 negative triangles 445: dt=0.9405, 22 negative triangles 446: dt=0.9405, 22 negative triangles 447: dt=0.9405, 19 negative triangles 448: dt=0.9405, 16 negative triangles 449: dt=0.9405, 18 negative triangles 450: dt=0.9405, 15 negative triangles 451: dt=0.9405, 15 negative triangles 452: dt=0.9405, 15 negative triangles 453: dt=0.9405, 12 negative triangles 454: dt=0.9405, 13 negative triangles 455: dt=0.9405, 13 negative triangles 456: dt=0.9405, 10 negative triangles 457: dt=0.9405, 8 negative triangles 458: dt=0.9405, 9 negative triangles 459: dt=0.9405, 10 negative triangles 460: dt=0.9405, 11 negative triangles 461: dt=0.9405, 10 negative triangles 462: dt=0.9405, 8 negative triangles 463: dt=0.9405, 9 negative triangles 464: dt=0.9405, 7 negative triangles 465: dt=0.9405, 7 negative triangles 466: dt=0.9405, 6 negative triangles 467: dt=0.9405, 8 negative triangles 468: dt=0.9405, 5 negative triangles 469: dt=0.9405, 4 negative triangles 470: dt=0.9405, 1 negative triangles 471: dt=0.9405, 2 negative triangles 472: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.97 hours mris_sphere utimesec 3898.742301 mris_sphere stimesec 0.197969 mris_sphere ru_maxrss 234000 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38741 mris_sphere ru_majflt 3 mris_sphere ru_nswap 0 mris_sphere ru_inblock 12512 mris_sphere ru_oublock 9328 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 361 mris_sphere ru_nivcsw 323023 FSRUNTIME@ mris_sphere 1.9669 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.306... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %22.00 pass 1: epoch 2 of 3 starting distance error %21.86 unfolding complete - removing small folds... starting distance error %21.46 removing remaining folds... final distance error %21.52 MRISunfold() return, current seed 1234 -01: dt=0.0000, 379 negative triangles 286: dt=0.9900, 379 negative triangles 287: dt=0.9900, 164 negative triangles 288: dt=0.9900, 116 negative triangles 289: dt=0.9900, 109 negative triangles 290: dt=0.9900, 88 negative triangles 291: dt=0.9900, 83 negative triangles 292: dt=0.9900, 85 negative triangles 293: dt=0.9900, 73 negative triangles 294: dt=0.9900, 70 negative triangles 295: dt=0.9900, 59 negative triangles 296: dt=0.9900, 60 negative triangles 297: dt=0.9900, 50 negative triangles 298: dt=0.9900, 46 negative triangles 299: dt=0.9900, 48 negative triangles 300: dt=0.9900, 33 negative triangles 301: dt=0.9900, 35 negative triangles 302: dt=0.9900, 35 negative triangles 303: dt=0.9900, 37 negative triangles 304: dt=0.9900, 24 negative triangles 305: dt=0.9900, 23 negative triangles 306: dt=0.9900, 18 negative triangles 307: dt=0.9900, 29 negative triangles 308: dt=0.9900, 18 negative triangles 309: dt=0.9900, 15 negative triangles 310: dt=0.9900, 13 negative triangles 311: dt=0.9900, 11 negative triangles 312: dt=0.9900, 13 negative triangles 313: dt=0.9900, 7 negative triangles 314: dt=0.9900, 4 negative triangles 315: dt=0.9900, 7 negative triangles 316: dt=0.9900, 4 negative triangles 317: dt=0.9900, 3 negative triangles 318: dt=0.9900, 2 negative triangles 319: dt=0.9900, 3 negative triangles 320: dt=0.9900, 1 negative triangles 321: dt=0.9900, 1 negative triangles 322: dt=0.9900, 3 negative triangles 323: dt=0.9900, 1 negative triangles 324: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.77 hours mris_sphere utimesec 3185.240769 mris_sphere stimesec 0.217966 mris_sphere ru_maxrss 230624 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 37913 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9192 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 90 mris_sphere ru_nivcsw 321031 FSRUNTIME@ mris_sphere 1.7688 hours 1 threads PIDs (26369 26372) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 29 05:57:18 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sun Oct 29 05:57:18 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 31117 of (31117 31120) to complete... Waiting for PID 31120 of (31117 31120) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.615 curvature mean = 0.025, std = 0.812 curvature mean = 0.011, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 8.00) sse = 288392.7, tmin=4.0424 d=16.00 min @ (4.00, 4.00, -4.00) sse = 267206.1, tmin=6.1104 d=8.00 min @ (0.00, 0.00, 2.00) sse = 265042.0, tmin=8.2699 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 264453.8, tmin=10.4455 d=2.00 min @ (0.50, 0.00, -0.50) sse = 264361.6, tmin=12.6226 d=1.00 min @ (-0.25, 0.00, 0.25) sse = 264325.9, tmin=14.7681 d=0.50 min @ (0.12, 0.00, 0.00) sse = 264310.7, tmin=16.9017 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 16.90 min curvature mean = -0.000, std = 0.839 curvature mean = 0.004, std = 0.948 curvature mean = -0.002, std = 0.850 curvature mean = 0.001, std = 0.979 curvature mean = -0.002, std = 0.853 curvature mean = 0.000, std = 0.991 2 Reading smoothwm curvature mean = -0.043, std = 0.423 curvature mean = 0.039, std = 0.244 curvature mean = 0.065, std = 0.243 curvature mean = 0.034, std = 0.306 curvature mean = 0.056, std = 0.360 curvature mean = 0.032, std = 0.333 curvature mean = 0.036, std = 0.475 curvature mean = 0.031, std = 0.344 curvature mean = 0.016, std = 0.584 MRISregister() return, current seed 0 -01: dt=0.0000, 380 negative triangles 137: dt=0.9900, 380 negative triangles expanding nbhd size to 1 138: dt=0.9900, 458 negative triangles 139: dt=0.9900, 399 negative triangles 140: dt=0.9405, 406 negative triangles 141: dt=0.9405, 389 negative triangles 142: dt=0.9405, 391 negative triangles 143: dt=0.9405, 374 negative triangles 144: dt=0.9405, 371 negative triangles 145: dt=0.9405, 358 negative triangles 146: dt=0.9405, 346 negative triangles 147: dt=0.9405, 323 negative triangles 148: dt=0.9405, 300 negative triangles 149: dt=0.9405, 286 negative triangles 150: dt=0.9405, 273 negative triangles 151: dt=0.9405, 262 negative triangles 152: dt=0.9405, 262 negative triangles 153: dt=0.9405, 250 negative triangles 154: dt=0.9405, 236 negative triangles 155: dt=0.9405, 211 negative triangles 156: dt=0.9405, 216 negative triangles 157: dt=0.9405, 209 negative triangles 158: dt=0.9405, 198 negative triangles 159: dt=0.9405, 202 negative triangles 160: dt=0.9405, 189 negative triangles 161: dt=0.9405, 179 negative triangles 162: dt=0.9405, 171 negative triangles 163: dt=0.9405, 164 negative triangles 164: dt=0.9405, 161 negative triangles 165: dt=0.9405, 149 negative triangles 166: dt=0.9405, 147 negative triangles 167: dt=0.9405, 142 negative triangles 168: dt=0.9405, 151 negative triangles 169: dt=0.9405, 131 negative triangles 170: dt=0.9405, 128 negative triangles 171: dt=0.9405, 130 negative triangles 172: dt=0.9405, 119 negative triangles 173: dt=0.9405, 109 negative triangles 174: dt=0.9405, 97 negative triangles 175: dt=0.9405, 90 negative triangles 176: dt=0.9405, 80 negative triangles 177: dt=0.9405, 74 negative triangles 178: dt=0.9405, 78 negative triangles 179: dt=0.9405, 67 negative triangles 180: dt=0.9405, 65 negative triangles 181: dt=0.9405, 58 negative triangles 182: dt=0.9405, 58 negative triangles 183: dt=0.9405, 47 negative triangles 184: dt=0.9405, 45 negative triangles 185: dt=0.9405, 47 negative triangles 186: dt=0.9405, 43 negative triangles 187: dt=0.9405, 47 negative triangles 188: dt=0.9405, 38 negative triangles 189: dt=0.9405, 37 negative triangles 190: dt=0.9405, 34 negative triangles 191: dt=0.9405, 32 negative triangles 192: dt=0.9405, 31 negative triangles 193: dt=0.9405, 27 negative triangles 194: dt=0.9405, 25 negative triangles 195: dt=0.9405, 24 negative triangles 196: dt=0.9405, 26 negative triangles 197: dt=0.9405, 19 negative triangles 198: dt=0.9405, 16 negative triangles 199: dt=0.9405, 15 negative triangles 200: dt=0.9405, 14 negative triangles 201: dt=0.9405, 11 negative triangles 202: dt=0.9405, 11 negative triangles 203: dt=0.9405, 10 negative triangles 204: dt=0.9405, 10 negative triangles 205: dt=0.9405, 10 negative triangles 206: dt=0.9405, 10 negative triangles 207: dt=0.9405, 10 negative triangles 208: dt=0.9405, 10 negative triangles 209: dt=0.9405, 9 negative triangles 210: dt=0.9405, 8 negative triangles 211: dt=0.9405, 8 negative triangles 212: dt=0.9405, 8 negative triangles 213: dt=0.9405, 12 negative triangles 214: dt=0.9405, 10 negative triangles 215: dt=0.9405, 8 negative triangles 216: dt=0.9405, 8 negative triangles 217: dt=0.9405, 7 negative triangles 218: dt=0.9405, 10 negative triangles 219: dt=0.9405, 9 negative triangles 220: dt=0.9405, 8 negative triangles 221: dt=0.9405, 4 negative triangles 222: dt=0.9405, 5 negative triangles 223: dt=0.9405, 4 negative triangles 224: dt=0.9405, 4 negative triangles 225: dt=0.9405, 5 negative triangles 226: dt=0.9405, 5 negative triangles 227: dt=0.9405, 4 negative triangles 228: dt=0.9405, 3 negative triangles 229: dt=0.9405, 2 negative triangles 230: dt=0.9405, 2 negative triangles 231: dt=0.9405, 2 negative triangles 232: dt=0.9405, 2 negative triangles 233: dt=0.9405, 2 negative triangles 234: dt=0.9405, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.82 hours mris_register utimesec 3507.351801 mris_register stimesec 0.635903 mris_register ru_maxrss 225856 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 31888 mris_register ru_majflt 3 mris_register ru_nswap 0 mris_register ru_inblock 18120 mris_register ru_oublock 9336 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 390 mris_register ru_nivcsw 308047 FSRUNTIME@ mris_register 1.8192 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.640 curvature mean = 0.027, std = 0.812 curvature mean = 0.010, std = 0.870 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 314626.8, tmin=1.9876 d=32.00 min @ (8.00, 8.00, -8.00) sse = 246616.2, tmin=4.0327 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 229902.5, tmin=6.1086 d=8.00 min @ (0.00, 2.00, 2.00) sse = 218453.6, tmin=8.1946 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 218045.2, tmin=10.2961 d=2.00 min @ (0.50, 0.50, 0.00) sse = 217782.4, tmin=12.4060 d=1.00 min @ (0.00, -0.25, -0.25) sse = 217608.5, tmin=14.5096 d=0.50 min @ (0.12, 0.12, 0.00) sse = 217580.7, tmin=16.6252 tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 16.63 min curvature mean = -0.004, std = 0.826 curvature mean = 0.005, std = 0.950 curvature mean = -0.008, std = 0.834 curvature mean = 0.003, std = 0.979 curvature mean = -0.009, std = 0.836 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.045, std = 0.419 curvature mean = 0.033, std = 0.237 curvature mean = 0.072, std = 0.251 curvature mean = 0.026, std = 0.298 curvature mean = 0.059, std = 0.367 curvature mean = 0.025, std = 0.325 curvature mean = 0.037, std = 0.482 curvature mean = 0.024, std = 0.337 curvature mean = 0.015, std = 0.591 MRISregister() return, current seed 0 -01: dt=0.0000, 347 negative triangles 131: dt=0.9900, 347 negative triangles expanding nbhd size to 1 132: dt=0.9900, 461 negative triangles 133: dt=0.9900, 357 negative triangles 134: dt=0.9900, 362 negative triangles 135: dt=0.9900, 363 negative triangles 136: dt=0.9900, 353 negative triangles 137: dt=0.9900, 351 negative triangles 138: dt=0.9900, 331 negative triangles 139: dt=0.9900, 311 negative triangles 140: dt=0.9900, 306 negative triangles 141: dt=0.9900, 283 negative triangles 142: dt=0.9900, 263 negative triangles 143: dt=0.9900, 255 negative triangles 144: dt=0.9900, 243 negative triangles 145: dt=0.9900, 236 negative triangles 146: dt=0.9900, 232 negative triangles 147: dt=0.9900, 217 negative triangles 148: dt=0.9900, 201 negative triangles 149: dt=0.9900, 188 negative triangles 150: dt=0.9900, 171 negative triangles 151: dt=0.9900, 160 negative triangles 152: dt=0.9900, 164 negative triangles 153: dt=0.9900, 149 negative triangles 154: dt=0.9900, 148 negative triangles 155: dt=0.9900, 138 negative triangles 156: dt=0.9900, 132 negative triangles 157: dt=0.9900, 124 negative triangles 158: dt=0.9900, 124 negative triangles 159: dt=0.9900, 121 negative triangles 160: dt=0.9900, 109 negative triangles 161: dt=0.9900, 99 negative triangles 162: dt=0.9900, 102 negative triangles 163: dt=0.9900, 96 negative triangles 164: dt=0.9900, 91 negative triangles 165: dt=0.9900, 94 negative triangles 166: dt=0.9900, 87 negative triangles 167: dt=0.9900, 80 negative triangles 168: dt=0.9900, 77 negative triangles 169: dt=0.9900, 71 negative triangles 170: dt=0.9900, 65 negative triangles 171: dt=0.9900, 66 negative triangles 172: dt=0.9900, 66 negative triangles 173: dt=0.9900, 68 negative triangles 174: dt=0.9900, 73 negative triangles 175: dt=0.9900, 74 negative triangles 176: dt=0.9900, 67 negative triangles 177: dt=0.9900, 61 negative triangles 178: dt=0.9900, 55 negative triangles 179: dt=0.9900, 52 negative triangles 180: dt=0.9900, 49 negative triangles 181: dt=0.9900, 43 negative triangles 182: dt=0.9900, 41 negative triangles 183: dt=0.9900, 43 negative triangles 184: dt=0.9900, 44 negative triangles 185: dt=0.9900, 42 negative triangles 186: dt=0.9900, 42 negative triangles 187: dt=0.9900, 38 negative triangles 188: dt=0.9900, 43 negative triangles 189: dt=0.9900, 48 negative triangles 190: dt=0.9900, 43 negative triangles 191: dt=0.9900, 42 negative triangles 192: dt=0.9900, 42 negative triangles 193: dt=0.9900, 31 negative triangles 194: dt=0.9900, 31 negative triangles 195: dt=0.9900, 31 negative triangles 196: dt=0.9900, 27 negative triangles 197: dt=0.9900, 28 negative triangles 198: dt=0.9900, 29 negative triangles 199: dt=0.9900, 26 negative triangles 200: dt=0.9900, 24 negative triangles 201: dt=0.9900, 23 negative triangles 202: dt=0.9900, 27 negative triangles 203: dt=0.9900, 30 negative triangles 204: dt=0.9900, 25 negative triangles 205: dt=0.9900, 22 negative triangles 206: dt=0.9900, 19 negative triangles 207: dt=0.9900, 20 negative triangles 208: dt=0.9900, 21 negative triangles 209: dt=0.9900, 19 negative triangles 210: dt=0.9900, 22 negative triangles 211: dt=0.9900, 23 negative triangles 212: dt=0.9900, 17 negative triangles 213: dt=0.9900, 18 negative triangles 214: dt=0.9900, 19 negative triangles 215: dt=0.9900, 17 negative triangles 216: dt=0.9900, 17 negative triangles 217: dt=0.9900, 20 negative triangles 218: dt=0.9900, 22 negative triangles 219: dt=0.9900, 17 negative triangles 220: dt=0.9900, 16 negative triangles 221: dt=0.9900, 15 negative triangles 222: dt=0.9900, 15 negative triangles 223: dt=0.9900, 15 negative triangles 224: dt=0.9900, 16 negative triangles 225: dt=0.9900, 18 negative triangles 226: dt=0.9900, 16 negative triangles 227: dt=0.9900, 15 negative triangles 228: dt=0.9900, 15 negative triangles 229: dt=0.9900, 15 negative triangles 230: dt=0.9900, 14 negative triangles 231: dt=0.9900, 13 negative triangles 232: dt=0.9900, 14 negative triangles 233: dt=0.9900, 14 negative triangles 234: dt=0.9900, 13 negative triangles 235: dt=0.9900, 12 negative triangles 236: dt=0.9900, 12 negative triangles 237: dt=0.9900, 12 negative triangles 238: dt=0.9900, 11 negative triangles 239: dt=0.9900, 11 negative triangles 240: dt=0.9900, 11 negative triangles 241: dt=0.9900, 11 negative triangles 242: dt=0.9900, 10 negative triangles 243: dt=0.9900, 10 negative triangles 244: dt=0.9900, 8 negative triangles 245: dt=0.9900, 8 negative triangles 246: dt=0.9900, 7 negative triangles 247: dt=0.9900, 7 negative triangles 248: dt=0.9900, 7 negative triangles 249: dt=0.9900, 6 negative triangles 250: dt=0.9900, 6 negative triangles 251: dt=0.9900, 4 negative triangles 252: dt=0.9900, 1 negative triangles 253: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.69 hours mris_register utimesec 3043.867261 mris_register stimesec 0.287956 mris_register ru_maxrss 221236 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 30207 mris_register ru_majflt 1 mris_register ru_nswap 0 mris_register ru_inblock 8168 mris_register ru_oublock 9248 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 472 mris_register ru_nivcsw 306417 FSRUNTIME@ mris_register 1.6904 hours 1 threads PIDs (31117 31120) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 29 07:46:27 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 29 07:46:27 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 3325 of (3325 3328) to complete... Waiting for PID 3328 of (3325 3328) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (3325 3328) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 29 07:46:30 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Sun Oct 29 07:46:30 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 3367 of (3367 3370) to complete... Waiting for PID 3370 of (3367 3370) to complete... mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (3367 3370) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 29 07:46:34 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Sun Oct 29 07:46:34 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 3413 of (3413 3416) to complete... Waiting for PID 3416 of (3413 3416) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1175 labels changed using aseg relabeling using gibbs priors... 000: 3029 changed, 131248 examined... 001: 740 changed, 12883 examined... 002: 173 changed, 4062 examined... 003: 72 changed, 1049 examined... 004: 35 changed, 443 examined... 005: 13 changed, 190 examined... 006: 8 changed, 78 examined... 007: 4 changed, 51 examined... 008: 1 changed, 22 examined... 009: 0 changed, 7 examined... 225 labels changed using aseg 000: 126 total segments, 83 labels (515 vertices) changed 001: 43 total segments, 1 labels (2 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1447 vertices marked for relabeling... 1447 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 33 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1026 labels changed using aseg relabeling using gibbs priors... 000: 2646 changed, 129560 examined... 001: 600 changed, 11404 examined... 002: 157 changed, 3458 examined... 003: 64 changed, 918 examined... 004: 33 changed, 368 examined... 005: 13 changed, 207 examined... 006: 5 changed, 77 examined... 007: 0 changed, 27 examined... 130 labels changed using aseg 000: 96 total segments, 57 labels (219 vertices) changed 001: 40 total segments, 1 labels (1 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1307 vertices marked for relabeling... 1307 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 37 seconds. PIDs (3413 3416) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 29 07:47:10 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 29 07:47:10 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 rh Waiting for PID 3478 of (3478 3481) to complete... Waiting for PID 3481 of (3478 3481) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... 23908 bright wm thresholded. 4134 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig... computing class statistics... border white: 256030 voxels (1.53%) border gray 340019 voxels (2.03%) WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0] GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70) setting MAX_BORDER_WHITE to 104.9 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 40.8 (was 40) setting MAX_GRAY to 87.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=96+-8.7, GM=63+-8.7 mean inside = 89.3, mean outside = 71.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.32 (0.02-->11.65) (max @ vno 57431 --> 125716) face area 0.35 +- 0.23 (0.00-->18.31) mean absolute distance = 0.57 +- 0.92 3553 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 178 points - only 0.00% unknown deleting segment 1 with 20 points - only 0.00% unknown deleting segment 2 with 38 points - only 0.00% unknown deleting segment 3 with 83 points - only 0.00% unknown deleting segment 4 with 110 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 81 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 21 points - only 0.00% unknown deleting segment 12 with 35 points - only 0.00% unknown deleting segment 13 with 35 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown deleting segment 17 with 62 points - only 0.00% unknown deleting segment 18 with 11 points - only 0.00% unknown deleting segment 19 with 5 points - only 0.00% unknown deleting segment 20 with 7 points - only 0.00% unknown deleting segment 21 with 11 points - only 0.00% unknown deleting segment 22 with 24 points - only 0.00% unknown deleting segment 23 with 126 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 24 with 2 points - only 0.00% unknown deleting segment 26 with 40 points - only 0.00% unknown deleting segment 27 with 96 points - only 0.00% unknown mean border=75.4, 419 (418) missing vertices, mean dist 0.2 [0.8 (%19.8)->0.5 (%80.2))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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 0.94 +- 0.33 (0.05-->11.61) (max @ vno 57431 --> 125716) face area 0.35 +- 0.23 (0.00-->17.67) mean absolute distance = 0.38 +- 0.68 3711 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1784046.5, rms=6.571 001: dt: 0.5000, sse=1211239.4, rms=4.467 (32.020%) 002: dt: 0.5000, sse=1081838.9, rms=3.922 (12.207%) rms = 3.98, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=966111.8, rms=3.285 (16.234%) 004: dt: 0.2500, sse=925156.8, rms=3.008 (8.421%) 005: dt: 0.2500, sse=916870.3, rms=2.892 (3.870%) 006: dt: 0.2500, sse=910641.8, rms=2.841 (1.776%) 007: dt: 0.2500, sse=899266.7, rms=2.790 (1.773%) rms = 2.75, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=891174.9, rms=2.754 (1.294%) 009: dt: 0.1250, sse=880523.9, rms=2.690 (2.326%) rms = 2.67, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=877732.5, rms=2.667 (0.867%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 188 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 2 with 34 points - only 0.00% unknown deleting segment 3 with 107 points - only 0.00% unknown deleting segment 4 with 83 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 71 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 21 points - only 0.00% unknown deleting segment 12 with 27 points - only 0.00% unknown deleting segment 13 with 31 points - only 0.00% unknown deleting segment 14 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 7 points - only 0.00% unknown deleting segment 17 with 11 points - only 0.00% unknown deleting segment 18 with 27 points - only 0.00% unknown deleting segment 19 with 47 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 20 with 2 points - only 0.00% unknown deleting segment 21 with 33 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 22 with 3 points - only 0.00% unknown deleting segment 23 with 103 points - only 0.00% unknown mean border=78.0, 541 (171) missing vertices, mean dist -0.2 [0.4 (%67.8)->0.3 (%32.2))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 0.93 +- 0.33 (0.07-->11.58) (max @ vno 57431 --> 125716) face area 0.37 +- 0.24 (0.00-->18.79) mean absolute distance = 0.29 +- 0.49 3131 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1166963.6, rms=4.199 011: dt: 0.5000, sse=1007663.9, rms=3.214 (23.467%) rms = 3.41, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=903943.8, rms=2.623 (18.366%) 013: dt: 0.2500, sse=865633.2, rms=2.342 (10.725%) 014: dt: 0.2500, sse=860791.3, rms=2.255 (3.715%) rms = 2.23, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=859675.4, rms=2.229 (1.155%) 016: dt: 0.1250, sse=845289.5, rms=2.160 (3.100%) rms = 2.15, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=840518.4, rms=2.146 (0.627%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 69 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 2 with 34 points - only 0.00% unknown deleting segment 3 with 135 points - only 0.00% unknown deleting segment 4 with 107 points - only 0.00% unknown deleting segment 5 with 83 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 71 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown deleting segment 12 with 26 points - only 0.00% unknown deleting segment 13 with 28 points - only 0.00% unknown deleting segment 14 with 27 points - only 0.00% unknown deleting segment 15 with 25 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 17 with 1 points - only 0.00% unknown deleting segment 18 with 7 points - only 0.00% unknown deleting segment 19 with 16 points - only 0.00% unknown deleting segment 20 with 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 21 with 4 points - only 0.00% unknown deleting segment 22 with 10 points - only 0.00% unknown deleting segment 23 with 27 points - only 0.00% unknown deleting segment 24 with 75 points - only 0.00% unknown deleting segment 25 with 9 points - only 0.00% unknown deleting segment 26 with 31 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 27 with 3 points - only 0.00% unknown deleting segment 28 with 105 points - only 0.00% unknown mean border=79.3, 695 (118) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.3 (%40.6))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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 0.93 +- 0.33 (0.06-->11.54) (max @ vno 57431 --> 125716) face area 0.36 +- 0.24 (0.00-->18.16) mean absolute distance = 0.28 +- 0.43 3434 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=911837.9, rms=2.823 rms = 2.88, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=850959.4, rms=2.320 (17.810%) 019: dt: 0.2500, sse=829013.2, rms=2.028 (12.583%) rms = 2.01, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=830651.0, rms=2.014 (0.733%) 021: dt: 0.1250, sse=806100.6, rms=1.919 (4.720%) rms = 1.90, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=803037.6, rms=1.900 (0.952%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 68 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 2 with 34 points - only 0.00% unknown deleting segment 3 with 117 points - only 0.00% unknown deleting segment 4 with 107 points - only 0.00% unknown deleting segment 5 with 83 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 71 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 27 points - only 0.00% unknown deleting segment 11 with 28 points - only 0.00% unknown deleting segment 12 with 28 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 25 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown deleting segment 18 with 16 points - only 0.00% unknown deleting segment 19 with 13 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 20 with 4 points - only 0.00% unknown deleting segment 21 with 11 points - only 0.00% unknown deleting segment 22 with 27 points - only 0.00% unknown deleting segment 23 with 82 points - only 0.00% unknown deleting segment 24 with 9 points - only 0.00% unknown deleting segment 25 with 32 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 26 with 3 points - only 0.00% unknown deleting segment 27 with 105 points - only 0.00% unknown mean border=80.0, 769 (103) missing vertices, mean dist -0.0 [0.3 (%52.7)->0.3 (%47.3))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=820344.4, rms=2.111 rms = 2.17, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=785463.9, rms=1.771 (16.115%) 024: dt: 0.2500, sse=771739.7, rms=1.596 (9.881%) rms = 1.62, time step reduction 2 of 3 to 0.125... rms = 1.57, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=767655.4, rms=1.570 (1.612%) positioning took 0.9 minutes generating cortex label... 12 non-cortical segments detected only using segment with 6519 vertices erasing segment 0 (vno[0] = 31010) erasing segment 1 (vno[0] = 32161) erasing segment 2 (vno[0] = 36478) erasing segment 4 (vno[0] = 54109) erasing segment 5 (vno[0] = 81973) erasing segment 6 (vno[0] = 82913) erasing segment 7 (vno[0] = 86065) erasing segment 8 (vno[0] = 88867) erasing segment 9 (vno[0] = 94720) erasing segment 10 (vno[0] = 96228) erasing segment 11 (vno[0] = 105551) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.area vertex spacing 0.92 +- 0.33 (0.02-->11.46) (max @ vno 57431 --> 125716) face area 0.36 +- 0.24 (0.00-->18.14) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 59 points - only 0.00% unknown deleting segment 1 with 32 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=51.2, 400 (400) missing vertices, mean dist 1.4 [1.0 (%0.0)->3.0 (%100.0))] % 8 local maxima, %37 large gradients and %51 min vals, 965 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=tars-, 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=22523430.0, rms=29.506 001: dt: 0.0500, sse=19921118.0, rms=27.691 (6.152%) 002: dt: 0.0500, sse=18041402.0, rms=26.301 (5.017%) 003: dt: 0.0500, sse=16590684.0, rms=25.176 (4.277%) 004: dt: 0.0500, sse=15412776.0, rms=24.225 (3.781%) 005: dt: 0.0500, sse=14422604.0, rms=23.394 (3.427%) 006: dt: 0.0500, sse=13568109.0, rms=22.653 (3.167%) 007: dt: 0.0500, sse=12815069.0, rms=21.980 (2.974%) 008: dt: 0.0500, sse=12144431.0, rms=21.362 (2.812%) 009: dt: 0.0500, sse=11538691.0, rms=20.788 (2.687%) 010: dt: 0.0500, sse=10988115.0, rms=20.252 (2.578%) positioning took 1.8 minutes mean border=51.0, 401 (216) missing vertices, mean dist 1.2 [0.2 (%0.2)->2.6 (%99.8))] % 9 local maxima, %37 large gradients and %49 min vals, 922 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=11914375.0, rms=21.141 011: dt: 0.0500, sse=11400633.0, rms=20.650 (2.320%) 012: dt: 0.0500, sse=10929284.0, rms=20.190 (2.230%) 013: dt: 0.0500, sse=10493866.0, rms=19.754 (2.155%) 014: dt: 0.0500, sse=10093185.0, rms=19.345 (2.071%) 015: dt: 0.0500, sse=9721563.0, rms=18.958 (2.003%) 016: dt: 0.0500, sse=9378128.0, rms=18.593 (1.927%) 017: dt: 0.0500, sse=9060223.0, rms=18.248 (1.854%) 018: dt: 0.0500, sse=8765371.0, rms=17.922 (1.785%) 019: dt: 0.0500, sse=8490959.0, rms=17.613 (1.723%) 020: dt: 0.0500, sse=8235264.0, rms=17.321 (1.662%) positioning took 1.8 minutes mean border=50.9, 466 (165) missing vertices, mean dist 1.1 [0.1 (%2.1)->2.3 (%97.9))] % 9 local maxima, %38 large gradients and %49 min vals, 914 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=8358297.5, rms=17.468 021: dt: 0.0500, sse=8111856.5, rms=17.183 (1.628%) 022: dt: 0.0500, sse=7883419.0, rms=16.915 (1.559%) 023: dt: 0.0500, sse=7669262.0, rms=16.660 (1.509%) 024: dt: 0.0500, sse=7470349.5, rms=16.419 (1.445%) 025: dt: 0.0500, sse=7284163.5, rms=16.191 (1.392%) 026: dt: 0.0500, sse=7110500.5, rms=15.975 (1.336%) 027: dt: 0.0500, sse=6947347.0, rms=15.769 (1.289%) 028: dt: 0.0500, sse=6792784.0, rms=15.571 (1.254%) 029: dt: 0.0500, sse=6646514.0, rms=15.381 (1.218%) 030: dt: 0.0500, sse=6507681.0, rms=15.199 (1.185%) positioning took 1.8 minutes mean border=50.9, 546 (139) missing vertices, mean dist 1.0 [0.1 (%11.0)->2.2 (%89.0))] % 9 local maxima, %38 large gradients and %48 min vals, 809 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=6568624.5, rms=15.279 031: dt: 0.5000, sse=5568462.0, rms=13.907 (8.978%) 032: dt: 0.5000, sse=4921412.5, rms=12.934 (7.000%) 033: dt: 0.5000, sse=4449370.0, rms=12.175 (5.867%) 034: dt: 0.5000, sse=4104504.0, rms=11.582 (4.867%) 035: dt: 0.5000, sse=3809564.5, rms=11.053 (4.567%) 036: dt: 0.5000, sse=3554665.8, rms=10.572 (4.352%) 037: dt: 0.5000, sse=3306390.0, rms=10.086 (4.597%) 038: dt: 0.5000, sse=3079537.2, rms=9.621 (4.615%) 039: dt: 0.5000, sse=2870288.2, rms=9.173 (4.654%) 040: dt: 0.5000, sse=2698777.8, rms=8.787 (4.206%) 041: dt: 0.5000, sse=2548886.8, rms=8.438 (3.973%) 042: dt: 0.5000, sse=2440727.8, rms=8.175 (3.116%) 043: dt: 0.5000, sse=2350467.0, rms=7.951 (2.740%) 044: dt: 0.5000, sse=2289422.0, rms=7.793 (1.991%) 045: dt: 0.5000, sse=2241339.0, rms=7.668 (1.599%) 046: dt: 0.5000, sse=2209147.0, rms=7.580 (1.148%) 047: dt: 0.5000, sse=2179584.0, rms=7.502 (1.034%) 048: dt: 0.5000, sse=2158639.8, rms=7.443 (0.787%) 049: dt: 0.5000, sse=2139878.0, rms=7.392 (0.683%) rms = 7.35, time step reduction 1 of 3 to 0.250... 050: dt: 0.5000, sse=2125075.5, rms=7.349 (0.578%) 051: dt: 0.2500, sse=2047654.8, rms=7.109 (3.270%) 052: dt: 0.2500, sse=2015584.5, rms=7.018 (1.283%) rms = 7.03, time step reduction 2 of 3 to 0.125... rms = 6.98, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=2002416.9, rms=6.978 (0.567%) positioning took 6.1 minutes mean border=50.0, 3860 (56) missing vertices, mean dist 0.2 [0.2 (%47.2)->1.0 (%52.8))] %17 local maxima, %31 large gradients and %45 min vals, 407 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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=2241410.2, rms=6.947 054: dt: 0.5000, sse=2162338.0, rms=6.725 (3.188%) 055: dt: 0.5000, sse=2067294.0, rms=6.459 (3.964%) rms = 6.53, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1973017.1, rms=6.133 (5.040%) 057: dt: 0.2500, sse=1960439.1, rms=6.082 (0.840%) rms = 6.10, time step reduction 2 of 3 to 0.125... 058: dt: 0.1250, sse=1942388.6, rms=6.018 (1.043%) 059: dt: 0.1250, sse=1919217.4, rms=5.936 (1.364%) rms = 5.90, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1908110.8, rms=5.899 (0.627%) positioning took 2.5 minutes mean border=49.4, 4485 (48) missing vertices, mean dist 0.2 [0.2 (%47.5)->0.8 (%52.5))] %24 local maxima, %23 large gradients and %45 min vals, 465 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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=1964299.2, rms=6.034 rms = 6.36, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1931356.9, rms=5.922 (1.856%) rms = 5.90, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1921573.0, rms=5.898 (0.404%) 063: dt: 0.1250, sse=1900245.1, rms=5.821 (1.309%) 064: dt: 0.1250, sse=1883896.8, rms=5.769 (0.899%) rms = 5.75, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1876085.2, rms=5.745 (0.409%) positioning took 1.9 minutes mean border=48.9, 7941 (45) missing vertices, mean dist 0.1 [0.2 (%46.7)->0.6 (%53.3))] %27 local maxima, %19 large gradients and %43 min vals, 534 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1901558.1, rms=5.791 rms = 5.98, time step reduction 1 of 3 to 0.250... 066: dt: 0.2500, sse=1872328.4, rms=5.691 (1.724%) 067: dt: 0.2500, sse=1841534.6, rms=5.602 (1.558%) rms = 5.59, time step reduction 2 of 3 to 0.125... 068: dt: 0.2500, sse=1833290.4, rms=5.585 (0.305%) 069: dt: 0.1250, sse=1785044.2, rms=5.405 (3.225%) 070: dt: 0.1250, sse=1764686.2, rms=5.335 (1.308%) rms = 5.31, time step reduction 3 of 3 to 0.062... 071: dt: 0.1250, sse=1757149.4, rms=5.310 (0.456%) positioning took 2.3 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.area.pial vertex spacing 1.09 +- 0.55 (0.06-->11.53) (max @ vno 57431 --> 125716) face area 0.46 +- 0.46 (0.00-->20.37) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 131248 vertices processed 25000 of 131248 vertices processed 50000 of 131248 vertices processed 75000 of 131248 vertices processed 100000 of 131248 vertices processed 125000 of 131248 vertices processed 0 of 131248 vertices processed 25000 of 131248 vertices processed 50000 of 131248 vertices processed 75000 of 131248 vertices processed 100000 of 131248 vertices processed 125000 of 131248 vertices processed thickness calculation complete, 527:2302 truncations. 21477 vertices at 0 distance 72580 vertices at 1 distance 81694 vertices at 2 distance 46447 vertices at 3 distance 18195 vertices at 4 distance 6328 vertices at 5 distance 2281 vertices at 6 distance 1000 vertices at 7 distance 482 vertices at 8 distance 274 vertices at 9 distance 136 vertices at 10 distance 138 vertices at 11 distance 105 vertices at 12 distance 62 vertices at 13 distance 60 vertices at 14 distance 35 vertices at 15 distance 49 vertices at 16 distance 26 vertices at 17 distance 31 vertices at 18 distance 40 vertices at 19 distance 48 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.thickness positioning took 30.7 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050418 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... 23908 bright wm thresholded. 4134 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig... computing class statistics... border white: 256030 voxels (1.53%) border gray 340019 voxels (2.03%) WM (93.0): 93.9 +- 8.9 [70.0 --> 110.0] GM (68.0) : 67.3 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.9 (was 70) setting MAX_BORDER_WHITE to 104.9 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 40.8 (was 40) setting MAX_GRAY to 87.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 29.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=96+-9.6, GM=63+-9.6 mean inside = 89.8, mean outside = 71.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.91 +- 0.30 (0.02-->9.81) (max @ vno 69448 --> 92233) face area 0.35 +- 0.20 (0.00-->14.24) mean absolute distance = 0.55 +- 0.85 3418 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 1 with 41 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 21 points - only 0.00% unknown deleting segment 5 with 50 points - only 0.00% unknown deleting segment 6 with 111 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 134 points - only 0.00% unknown deleting segment 12 with 46 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 33 points - only 0.00% unknown deleting segment 15 with 113 points - only 0.00% unknown deleting segment 16 with 43 points - only 0.00% unknown deleting segment 17 with 5 points - only 0.00% unknown deleting segment 18 with 11 points - only 0.00% unknown deleting segment 19 with 13 points - only 0.00% unknown deleting segment 20 with 83 points - only 0.00% unknown mean border=75.6, 261 (261) missing vertices, mean dist 0.3 [0.7 (%18.5)->0.5 (%81.5))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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 0.93 +- 0.30 (0.07-->9.82) (max @ vno 69448 --> 92233) face area 0.35 +- 0.20 (0.00-->13.90) mean absolute distance = 0.36 +- 0.63 3303 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1842870.9, rms=6.894 001: dt: 0.5000, sse=1161472.9, rms=4.459 (35.313%) 002: dt: 0.5000, sse=1015373.3, rms=3.785 (15.121%) rms = 3.79, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=899215.8, rms=3.091 (18.338%) 004: dt: 0.2500, sse=851830.9, rms=2.733 (11.575%) 005: dt: 0.2500, sse=835550.0, rms=2.580 (5.613%) 006: dt: 0.2500, sse=824682.8, rms=2.512 (2.622%) rms = 2.46, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=817734.1, rms=2.464 (1.924%) 008: dt: 0.1250, sse=810242.3, rms=2.402 (2.507%) rms = 2.38, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=807976.6, rms=2.379 (0.942%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 23 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 51 points - only 0.00% unknown deleting segment 5 with 99 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 92 points - only 0.00% unknown deleting segment 11 with 39 points - only 0.00% unknown deleting segment 12 with 36 points - only 0.00% unknown deleting segment 13 with 87 points - only 0.00% unknown deleting segment 14 with 10 points - only 0.00% unknown deleting segment 15 with 38 points - only 0.00% unknown deleting segment 16 with 11 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown deleting segment 18 with 59 points - only 0.00% unknown mean border=78.6, 278 (84) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.3 (%31.2))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 +- 0.30 (0.05-->9.83) (max @ vno 69448 --> 92233) face area 0.36 +- 0.21 (0.00-->15.04) mean absolute distance = 0.29 +- 0.48 3346 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1151385.6, rms=4.285 010: dt: 0.5000, sse=938254.7, rms=3.041 (29.026%) rms = 3.23, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=840086.6, rms=2.373 (21.954%) 012: dt: 0.2500, sse=803540.1, rms=2.024 (14.709%) 013: dt: 0.2500, sse=794332.7, rms=1.907 (5.788%) rms = 1.88, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=787078.1, rms=1.880 (1.421%) 015: dt: 0.1250, sse=780082.1, rms=1.818 (3.317%) rms = 1.81, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=777120.0, rms=1.810 (0.434%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 23 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 51 points - only 0.00% unknown deleting segment 5 with 100 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 93 points - only 0.00% unknown deleting segment 9 with 39 points - only 0.00% unknown deleting segment 10 with 37 points - only 0.00% unknown deleting segment 11 with 91 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 45 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 15 with 12 points - only 0.00% unknown deleting segment 16 with 62 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown mean border=80.1, 317 (51) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.3 (%40.1))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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 +- 0.30 (0.07-->9.82) (max @ vno 69448 --> 92233) face area 0.36 +- 0.21 (0.00-->14.88) mean absolute distance = 0.28 +- 0.42 3104 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=848647.4, rms=2.607 rms = 2.70, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=783880.3, rms=2.041 (21.714%) 018: dt: 0.2500, sse=756800.9, rms=1.709 (16.252%) rms = 1.67, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=752885.9, rms=1.665 (2.552%) 020: dt: 0.1250, sse=745662.1, rms=1.600 (3.919%) rms = 1.60, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=750865.8, rms=1.595 (0.302%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 51 points - only 0.00% unknown deleting segment 5 with 100 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 98 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown deleting segment 10 with 37 points - only 0.00% unknown deleting segment 11 with 104 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 45 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 11 points - only 0.00% unknown deleting segment 16 with 64 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown mean border=80.7, 384 (35) missing vertices, mean dist -0.0 [0.3 (%52.6)->0.3 (%47.4))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=765798.4, rms=1.833 rms = 1.91, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=727234.6, rms=1.444 (21.238%) 023: dt: 0.2500, sse=714266.5, rms=1.239 (14.224%) rms = 1.27, time step reduction 2 of 3 to 0.125... rms = 1.22, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=710467.0, rms=1.224 (1.180%) positioning took 0.8 minutes generating cortex label... 12 non-cortical segments detected only using segment with 6313 vertices erasing segment 0 (vno[0] = 31939) erasing segment 1 (vno[0] = 32998) erasing segment 3 (vno[0] = 76597) erasing segment 4 (vno[0] = 82670) erasing segment 5 (vno[0] = 82688) erasing segment 6 (vno[0] = 86088) erasing segment 7 (vno[0] = 86120) erasing segment 8 (vno[0] = 87128) erasing segment 9 (vno[0] = 93751) erasing segment 10 (vno[0] = 95923) erasing segment 11 (vno[0] = 96633) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.area vertex spacing 0.92 +- 0.30 (0.02-->9.82) (max @ vno 69448 --> 92233) face area 0.35 +- 0.21 (0.00-->14.70) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 10 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.8, 281 (281) missing vertices, mean dist 1.5 [1.7 (%0.0)->3.1 (%100.0))] % 8 local maxima, %39 large gradients and %49 min vals, 792 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=tars-, 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=23946122.0, rms=30.663 001: dt: 0.0500, sse=21225300.0, rms=28.815 (6.026%) 002: dt: 0.0500, sse=19254408.0, rms=27.399 (4.916%) 003: dt: 0.0500, sse=17732704.0, rms=26.252 (4.183%) 004: dt: 0.0500, sse=16497728.0, rms=25.284 (3.689%) 005: dt: 0.0500, sse=15456960.0, rms=24.438 (3.346%) 006: dt: 0.0500, sse=14556396.0, rms=23.682 (3.095%) 007: dt: 0.0500, sse=13762728.0, rms=22.994 (2.903%) 008: dt: 0.0500, sse=13052958.0, rms=22.362 (2.752%) 009: dt: 0.0500, sse=12412531.0, rms=21.775 (2.624%) 010: dt: 0.0500, sse=11828569.0, rms=21.226 (2.522%) positioning took 1.8 minutes mean border=50.5, 271 (153) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.6 (%99.9))] % 9 local maxima, %39 large gradients and %47 min vals, 723 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=12756315.0, rms=22.088 011: dt: 0.0500, sse=12211216.0, rms=21.584 (2.283%) 012: dt: 0.0500, sse=11710493.0, rms=21.110 (2.196%) 013: dt: 0.0500, sse=11248806.0, rms=20.663 (2.116%) 014: dt: 0.0500, sse=10821538.0, rms=20.241 (2.044%) 015: dt: 0.0500, sse=10426159.0, rms=19.842 (1.971%) 016: dt: 0.0500, sse=10060004.0, rms=19.465 (1.899%) 017: dt: 0.0500, sse=9720089.0, rms=19.109 (1.832%) 018: dt: 0.0500, sse=9404538.0, rms=18.772 (1.764%) 019: dt: 0.0500, sse=9111062.0, rms=18.453 (1.700%) 020: dt: 0.0500, sse=8837338.0, rms=18.150 (1.641%) positioning took 1.7 minutes mean border=50.4, 332 (127) missing vertices, mean dist 1.2 [0.1 (%1.9)->2.4 (%98.1))] % 9 local maxima, %40 large gradients and %47 min vals, 766 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=8960727.0, rms=18.293 021: dt: 0.0500, sse=8695920.0, rms=17.997 (1.615%) 022: dt: 0.0500, sse=8450954.0, rms=17.719 (1.544%) 023: dt: 0.0500, sse=8222297.0, rms=17.456 (1.487%) 024: dt: 0.0500, sse=8009258.0, rms=17.207 (1.427%) 025: dt: 0.0500, sse=7810915.0, rms=16.972 (1.368%) 026: dt: 0.0500, sse=7625615.5, rms=16.749 (1.314%) 027: dt: 0.0500, sse=7451650.5, rms=16.537 (1.267%) 028: dt: 0.0500, sse=7286212.5, rms=16.332 (1.236%) 029: dt: 0.0500, sse=7129248.0, rms=16.136 (1.203%) 030: dt: 0.0500, sse=6979744.0, rms=15.946 (1.174%) positioning took 1.8 minutes mean border=50.3, 360 (107) missing vertices, mean dist 1.1 [0.1 (%9.8)->2.3 (%90.2))] % 9 local maxima, %40 large gradients and %46 min vals, 733 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=7095884.5, rms=16.093 031: dt: 0.5000, sse=6008925.0, rms=14.659 (8.907%) 032: dt: 0.5000, sse=5277125.0, rms=13.601 (7.221%) 033: dt: 0.5000, sse=4723056.5, rms=12.741 (6.318%) 034: dt: 0.5000, sse=4308263.0, rms=12.052 (5.414%) 035: dt: 0.5000, sse=3961887.0, rms=11.446 (5.025%) 036: dt: 0.5000, sse=3667347.0, rms=10.903 (4.746%) 037: dt: 0.5000, sse=3392727.8, rms=10.374 (4.845%) 038: dt: 0.5000, sse=3151102.0, rms=9.885 (4.715%) 039: dt: 0.5000, sse=2920770.2, rms=9.398 (4.931%) 040: dt: 0.5000, sse=2726265.0, rms=8.965 (4.611%) 041: dt: 0.5000, sse=2560496.0, rms=8.580 (4.287%) 042: dt: 0.5000, sse=2437306.5, rms=8.280 (3.497%) 043: dt: 0.5000, sse=2338877.5, rms=8.034 (2.969%) 044: dt: 0.5000, sse=2269841.8, rms=7.855 (2.228%) 045: dt: 0.5000, sse=2222293.0, rms=7.731 (1.578%) 046: dt: 0.5000, sse=2182498.5, rms=7.623 (1.401%) 047: dt: 0.5000, sse=2152504.2, rms=7.543 (1.050%) 048: dt: 0.5000, sse=2130155.8, rms=7.479 (0.847%) rms = 7.44, time step reduction 1 of 3 to 0.250... 049: dt: 0.5000, sse=2113989.0, rms=7.435 (0.591%) 050: dt: 0.2500, sse=2020713.0, rms=7.148 (3.859%) 051: dt: 0.2500, sse=1981788.5, rms=7.037 (1.560%) rms = 7.03, time step reduction 2 of 3 to 0.125... 052: dt: 0.2500, sse=1981517.2, rms=7.034 (0.034%) 053: dt: 0.1250, sse=1948269.6, rms=6.933 (1.437%) rms = 6.90, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1938483.1, rms=6.904 (0.422%) positioning took 6.0 minutes mean border=49.4, 3039 (49) missing vertices, mean dist 0.2 [0.2 (%46.0)->0.9 (%54.0))] %17 local maxima, %32 large gradients and %44 min vals, 408 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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=2201920.0, rms=6.937 055: dt: 0.5000, sse=2119293.2, rms=6.707 (3.316%) 056: dt: 0.5000, sse=2018386.1, rms=6.417 (4.312%) rms = 6.47, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1907407.2, rms=6.030 (6.042%) 058: dt: 0.2500, sse=1886914.1, rms=5.950 (1.327%) rms = 5.95, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1867749.1, rms=5.880 (1.163%) 060: dt: 0.1250, sse=1840041.1, rms=5.780 (1.702%) rms = 5.75, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1830576.5, rms=5.747 (0.582%) positioning took 2.5 minutes mean border=48.7, 3640 (35) missing vertices, mean dist 0.2 [0.2 (%47.4)->0.7 (%52.6))] %26 local maxima, %24 large gradients and %44 min vals, 427 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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=1899533.0, rms=5.921 rms = 6.33, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1860729.8, rms=5.785 (2.289%) rms = 5.78, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1855363.8, rms=5.775 (0.170%) 064: dt: 0.1250, sse=1828287.9, rms=5.677 (1.698%) 065: dt: 0.1250, sse=1812861.4, rms=5.626 (0.896%) rms = 5.60, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1805326.9, rms=5.603 (0.415%) positioning took 1.9 minutes mean border=48.1, 7068 (33) missing vertices, mean dist 0.1 [0.2 (%47.5)->0.5 (%52.5))] %28 local maxima, %20 large gradients and %42 min vals, 458 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1840456.1, rms=5.683 rms = 5.95, time step reduction 1 of 3 to 0.250... 067: dt: 0.2500, sse=1809995.1, rms=5.577 (1.878%) 068: dt: 0.2500, sse=1783617.8, rms=5.502 (1.332%) rms = 5.52, time step reduction 2 of 3 to 0.125... rms = 5.45, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1771089.5, rms=5.454 (0.882%) positioning took 1.4 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.area.pial vertex spacing 1.09 +- 0.54 (0.04-->10.27) (max @ vno 52019 --> 127268) face area 0.47 +- 0.44 (0.00-->15.86) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 129560 vertices processed 25000 of 129560 vertices processed 50000 of 129560 vertices processed 75000 of 129560 vertices processed 100000 of 129560 vertices processed 125000 of 129560 vertices processed 0 of 129560 vertices processed 25000 of 129560 vertices processed 50000 of 129560 vertices processed 75000 of 129560 vertices processed 100000 of 129560 vertices processed 125000 of 129560 vertices processed thickness calculation complete, 578:2581 truncations. 21298 vertices at 0 distance 70949 vertices at 1 distance 80118 vertices at 2 distance 45914 vertices at 3 distance 18358 vertices at 4 distance 6532 vertices at 5 distance 2418 vertices at 6 distance 1054 vertices at 7 distance 482 vertices at 8 distance 263 vertices at 9 distance 219 vertices at 10 distance 153 vertices at 11 distance 92 vertices at 12 distance 68 vertices at 13 distance 61 vertices at 14 distance 44 vertices at 15 distance 35 vertices at 16 distance 22 vertices at 17 distance 26 vertices at 18 distance 26 vertices at 19 distance 34 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.thickness positioning took 29.9 minutes PIDs (3478 3481) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 29 08:17:53 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 0050418 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label Total face volume 275133 Total vertex volume 271693 (mask=0) #@# 0050418 lh 271693 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 29 08:17:57 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 0050418 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label Total face volume 276809 Total vertex volume 274048 (mask=0) #@# 0050418 rh 274048 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 29 08:18:00 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 0050418 SUBJECTS_DIR is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 298 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz mris_volmask took 13.03 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 29 08:31:01 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050418 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050418 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 29 08:31:01 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050418 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050418 rh pial Waiting for PID 5447 of (5447 5450 5453 5456) to complete... Waiting for PID 5450 of (5447 5450 5453 5456) to complete... Waiting for PID 5453 of (5447 5450 5453 5456) to complete... Waiting for PID 5456 of (5447 5450 5453 5456) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050418 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 275133 Total vertex volume 271693 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1312 1031 2467 2.521 0.637 0.135 0.036 16 2.3 bankssts 914 585 1643 2.375 0.803 0.112 0.022 10 0.7 caudalanteriorcingulate 3389 2343 8045 2.885 0.710 0.117 0.026 33 3.3 caudalmiddlefrontal 2601 1917 4343 2.058 0.534 0.171 0.056 49 6.3 cuneus 584 365 1372 2.760 1.016 0.150 0.067 13 1.7 entorhinal 4059 2961 8583 2.409 0.761 0.147 0.051 71 9.7 fusiform 5422 3982 12617 2.554 0.702 0.146 0.043 93 9.9 inferiorparietal 4301 3173 9122 2.529 0.849 0.146 0.047 74 9.5 inferiortemporal 1406 972 3079 2.495 1.109 0.135 0.041 20 2.2 isthmuscingulate 6621 4794 14180 2.350 0.718 0.165 0.054 128 14.8 lateraloccipital 3791 2585 7592 2.536 0.744 0.139 0.051 126 8.0 lateralorbitofrontal 3711 2774 6964 2.126 0.688 0.164 0.057 74 8.9 lingual 2269 1608 5307 2.734 0.799 0.156 0.051 51 4.9 medialorbitofrontal 4222 3269 10257 2.624 0.847 0.161 0.048 82 9.3 middletemporal 1075 725 2280 2.580 0.945 0.126 0.042 16 1.7 parahippocampal 2105 1502 3881 2.469 0.624 0.134 0.037 28 3.3 paracentral 1866 1419 4745 2.860 0.667 0.151 0.046 31 4.4 parsopercularis 840 664 2443 2.634 0.815 0.152 0.054 13 1.7 parsorbitalis 1517 1065 3958 2.869 0.602 0.128 0.035 27 2.6 parstriangularis 1987 1446 2535 1.843 0.605 0.157 0.055 36 4.7 pericalcarine 6891 4808 11539 2.176 0.805 0.138 0.041 90 12.4 postcentral 1513 1090 3424 2.757 0.858 0.135 0.029 21 1.8 posteriorcingulate 8689 5922 16727 2.481 0.795 0.135 0.041 129 15.6 precentral 6191 4476 13835 2.730 0.737 0.152 0.042 111 11.8 precuneus 999 711 2913 2.972 1.003 0.145 0.042 15 1.8 rostralanteriorcingulate 9292 6441 22617 2.790 0.698 0.137 0.042 159 16.6 rostralmiddlefrontal 10868 7872 28951 3.026 0.730 0.141 0.041 159 18.9 superiorfrontal 8232 5792 18058 2.548 0.671 0.142 0.038 116 13.0 superiorparietal 6020 4934 14149 2.532 0.912 0.153 0.052 137 15.3 superiortemporal 6155 4324 12308 2.623 0.739 0.144 0.045 99 11.9 supramarginal 417 287 1282 2.921 0.666 0.174 0.062 10 1.1 frontalpole 714 492 2402 3.264 0.889 0.144 0.051 14 1.7 temporalpole 463 417 1257 2.687 0.630 0.171 0.048 7 0.8 transversetemporal 3539 2359 6813 2.862 0.699 0.136 0.046 43 6.5 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050418 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 275133 Total vertex volume 271693 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1312 954 2467 2.521 0.637 0.162 0.053 45 2.8 bankssts 914 724 1643 2.375 0.803 0.153 0.040 14 1.7 caudalanteriorcingulate 3389 3119 8045 2.885 0.710 0.158 0.040 52 6.5 caudalmiddlefrontal 2601 2463 4343 2.058 0.534 0.179 0.050 53 5.9 cuneus 584 626 1372 2.760 1.016 0.194 0.057 10 1.5 entorhinal 4059 4033 8583 2.409 0.761 0.198 0.072 86 14.4 fusiform 5422 5874 12617 2.554 0.702 0.202 0.049 93 13.3 inferiorparietal 4301 4059 9122 2.529 0.849 0.188 0.057 81 12.0 inferiortemporal 1406 1341 3079 2.495 1.109 0.178 0.065 30 4.8 isthmuscingulate 6621 7033 14180 2.350 0.718 0.201 0.051 117 16.2 lateraloccipital 3791 3408 7592 2.536 0.744 0.189 0.059 66 10.6 lateralorbitofrontal 3711 3764 6964 2.126 0.688 0.196 0.055 67 9.7 lingual 2269 2240 5307 2.734 0.799 0.191 0.055 46 5.8 medialorbitofrontal 4222 4459 10257 2.624 0.847 0.187 0.044 66 9.2 middletemporal 1075 1060 2280 2.580 0.945 0.205 0.059 19 3.1 parahippocampal 2105 1663 3881 2.469 0.624 0.141 0.043 30 4.2 paracentral 1866 1978 4745 2.860 0.667 0.203 0.051 36 4.7 parsopercularis 840 1096 2443 2.634 0.815 0.238 0.064 14 2.5 parsorbitalis 1517 1657 3958 2.869 0.602 0.205 0.049 28 3.9 parstriangularis 1987 1415 2535 1.843 0.605 0.167 0.114 266 13.4 pericalcarine 6891 5702 11539 2.176 0.805 0.149 0.040 136 12.7 postcentral 1513 1316 3424 2.757 0.858 0.171 0.041 37 2.8 posteriorcingulate 8689 7255 16727 2.481 0.795 0.145 0.038 133 15.9 precentral 6191 5530 13835 2.730 0.737 0.179 0.048 132 14.3 precuneus 999 1202 2913 2.972 1.003 0.240 0.073 22 4.1 rostralanteriorcingulate 9292 9416 22617 2.790 0.698 0.186 0.047 175 20.6 rostralmiddlefrontal 10868 10978 28951 3.026 0.730 0.183 0.047 192 24.0 superiorfrontal 8232 8082 18058 2.548 0.671 0.177 0.045 139 17.1 superiorparietal 6020 6221 14149 2.532 0.912 0.179 0.047 101 13.0 superiortemporal 6155 5136 12308 2.623 0.739 0.167 0.051 144 13.8 supramarginal 417 584 1282 2.921 0.666 0.245 0.047 10 1.1 frontalpole 714 965 2402 3.264 0.889 0.233 0.066 15 2.2 temporalpole 463 485 1257 2.687 0.630 0.170 0.043 8 0.8 transversetemporal 3539 2462 6813 2.862 0.699 0.162 0.053 96 7.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050418 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 276809 Total vertex volume 274048 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1032 694 1842 2.524 0.680 0.091 0.020 5 0.7 bankssts 1056 706 2865 3.159 1.014 0.127 0.028 12 1.3 caudalanteriorcingulate 3248 2311 8682 3.121 0.647 0.129 0.032 36 4.4 caudalmiddlefrontal 2374 1715 4002 2.129 0.505 0.167 0.054 41 6.0 cuneus 370 305 1494 3.082 0.895 0.157 0.046 5 0.6 entorhinal 4019 2907 8171 2.225 0.728 0.154 0.049 72 8.6 fusiform 6721 4876 15078 2.527 0.776 0.147 0.042 105 12.4 inferiorparietal 3661 2700 8904 2.691 0.818 0.144 0.057 68 9.5 inferiortemporal 1165 792 2849 2.800 0.978 0.153 0.056 27 2.6 isthmuscingulate 7374 5205 15358 2.304 0.679 0.157 0.054 127 17.5 lateraloccipital 3893 2560 7440 2.570 0.843 0.144 0.052 58 8.8 lateralorbitofrontal 3272 2519 7511 2.511 0.695 0.163 0.051 56 6.7 lingual 2926 1990 6257 2.855 0.878 0.123 0.038 40 3.7 medialorbitofrontal 4903 3365 13051 3.029 0.780 0.130 0.041 71 8.4 middletemporal 819 574 1828 2.558 0.763 0.125 0.041 11 1.2 parahippocampal 1935 1353 3876 2.588 0.644 0.124 0.031 20 2.4 paracentral 1864 1335 3942 2.709 0.694 0.135 0.037 27 2.8 parsopercularis 1567 1102 4365 2.825 0.740 0.167 0.067 37 4.7 parsorbitalis 2125 1470 5238 2.863 0.718 0.134 0.044 33 3.6 parstriangularis 1786 1287 2873 2.259 0.641 0.151 0.048 24 3.1 pericalcarine 5903 3979 8673 1.950 0.603 0.117 0.033 64 7.4 postcentral 1622 1202 4147 2.928 0.878 0.155 0.040 28 2.6 posteriorcingulate 7728 5161 15839 2.700 0.735 0.125 0.041 95 14.2 precentral 5725 4025 11594 2.661 0.686 0.153 0.046 101 12.1 precuneus 997 706 2917 3.196 0.853 0.149 0.048 21 2.0 rostralanteriorcingulate 8971 6391 20914 2.688 0.702 0.153 0.051 175 20.3 rostralmiddlefrontal 11537 7997 29761 3.116 0.704 0.135 0.036 141 16.6 superiorfrontal 8491 5936 18250 2.480 0.686 0.138 0.038 126 14.1 superiorparietal 4951 3741 11632 2.705 0.766 0.134 0.042 69 9.1 superiortemporal 5980 4206 13587 2.800 0.686 0.142 0.041 89 9.9 supramarginal 626 392 1369 2.157 0.847 0.196 0.115 23 3.0 frontalpole 643 456 1558 2.554 0.910 0.177 0.079 14 2.1 temporalpole 477 318 904 2.622 0.655 0.158 0.055 10 1.0 transversetemporal 2903 2143 7225 3.029 0.994 0.127 0.037 29 4.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050418 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 276809 Total vertex volume 274048 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1032 690 1842 2.524 0.680 0.146 0.047 18 2.2 bankssts 1056 1012 2865 3.159 1.014 0.183 0.046 26 2.1 caudalanteriorcingulate 3248 3070 8682 3.121 0.647 0.160 0.041 59 5.9 caudalmiddlefrontal 2374 2216 4002 2.129 0.505 0.193 0.051 44 5.8 cuneus 370 608 1494 3.082 0.895 0.240 0.061 5 0.9 entorhinal 4019 4217 8171 2.225 0.728 0.209 0.069 84 11.5 fusiform 6721 6625 15078 2.527 0.776 0.193 0.051 117 16.3 inferiorparietal 3661 3771 8904 2.691 0.818 0.188 0.062 78 9.9 inferiortemporal 1165 1102 2849 2.800 0.978 0.199 0.074 54 4.4 isthmuscingulate 7374 7848 15358 2.304 0.679 0.202 0.056 132 18.8 lateraloccipital 3893 3215 7440 2.570 0.843 0.186 0.058 88 10.5 lateralorbitofrontal 3272 3558 7511 2.511 0.695 0.192 0.048 50 7.5 lingual 2926 2542 6257 2.855 0.878 0.171 0.049 67 6.3 medialorbitofrontal 4903 5145 13051 3.029 0.780 0.182 0.044 88 10.0 middletemporal 819 857 1828 2.558 0.763 0.207 0.061 13 2.3 parahippocampal 1935 1611 3876 2.588 0.644 0.149 0.039 35 3.2 paracentral 1864 1688 3942 2.709 0.694 0.162 0.045 48 3.7 parsopercularis 1567 1931 4365 2.825 0.740 0.215 0.052 39 3.9 parsorbitalis 2125 2141 5238 2.863 0.718 0.180 0.044 44 4.4 parstriangularis 1786 1252 2873 2.259 0.641 0.148 0.051 135 4.2 pericalcarine 5903 4860 8673 1.950 0.603 0.145 0.036 71 9.5 postcentral 1622 1499 4147 2.928 0.878 0.186 0.050 45 3.4 posteriorcingulate 7728 6256 15839 2.700 0.735 0.141 0.038 168 13.7 precentral 5725 4731 11594 2.661 0.686 0.180 0.059 178 13.5 precuneus 997 1051 2917 3.196 0.853 0.228 0.558 62 39.4 rostralanteriorcingulate 8971 9033 20914 2.688 0.702 0.196 0.054 190 23.5 rostralmiddlefrontal 11537 10848 29761 3.116 0.704 0.174 0.044 233 23.7 superiorfrontal 8491 8482 18250 2.480 0.686 0.183 0.048 144 20.3 superiorparietal 4951 5002 11632 2.705 0.766 0.182 0.064 110 17.0 superiortemporal 5980 5477 13587 2.800 0.686 0.166 0.043 103 12.3 supramarginal 626 725 1369 2.157 0.847 0.194 0.082 18 3.2 frontalpole 643 751 1558 2.554 0.910 0.241 0.075 15 2.1 temporalpole 477 352 904 2.622 0.655 0.138 0.338 165 1.6 transversetemporal 2903 2342 7225 3.029 0.994 0.187 0.061 88 8.1 insula PIDs (5447 5450 5453 5456) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 29 08:34:05 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Sun Oct 29 08:34:05 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 5599 of (5599 5602) to complete... Waiting for PID 5602 of (5599 5602) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 39 labels changed using aseg relabeling using gibbs priors... 000: 8713 changed, 131248 examined... 001: 2078 changed, 34314 examined... 002: 610 changed, 10810 examined... 003: 253 changed, 3448 examined... 004: 110 changed, 1421 examined... 005: 55 changed, 644 examined... 006: 32 changed, 329 examined... 007: 10 changed, 187 examined... 008: 1 changed, 68 examined... 009: 1 changed, 7 examined... 010: 1 changed, 8 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 0 changed, 8 examined... 0 labels changed using aseg 000: 285 total segments, 201 labels (2389 vertices) changed 001: 90 total segments, 7 labels (22 vertices) changed 002: 84 total segments, 1 labels (1 vertices) changed 003: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 31 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1172 vertices marked for relabeling... 1172 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 47 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 5 labels changed using aseg relabeling using gibbs priors... 000: 8535 changed, 129560 examined... 001: 1941 changed, 33460 examined... 002: 541 changed, 10353 examined... 003: 190 changed, 3080 examined... 004: 89 changed, 1163 examined... 005: 55 changed, 493 examined... 006: 28 changed, 299 examined... 007: 14 changed, 152 examined... 008: 10 changed, 70 examined... 009: 4 changed, 54 examined... 010: 5 changed, 25 examined... 011: 4 changed, 26 examined... 012: 2 changed, 20 examined... 013: 0 changed, 6 examined... 1 labels changed using aseg 000: 262 total segments, 177 labels (2619 vertices) changed 001: 94 total segments, 9 labels (29 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1073 vertices marked for relabeling... 1073 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 46 seconds. PIDs (5599 5602) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 29 08:34:52 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050418 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 29 08:34:52 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050418 rh white Waiting for PID 5664 of (5664 5667) to complete... Waiting for PID 5667 of (5664 5667) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050418 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 275133 Total vertex volume 271693 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1307 888 2738 2.586 0.785 0.143 0.051 23 2.7 G&S_frontomargin 1211 957 3518 2.625 0.824 0.168 0.052 24 2.5 G&S_occipital_inf 1713 1205 3272 2.273 0.726 0.151 0.049 46 3.9 G&S_paracentral 2484 1663 4286 2.368 0.802 0.149 0.058 41 6.2 G&S_subcentral 1008 736 2981 2.826 0.651 0.156 0.054 25 2.4 G&S_transv_frontopol 2422 1728 5918 2.945 0.739 0.136 0.037 32 4.0 G&S_cingul-Ant 1312 911 2687 2.842 0.673 0.105 0.021 8 1.3 G&S_cingul-Mid-Ant 1223 902 2881 3.119 0.492 0.127 0.030 11 1.5 G&S_cingul-Mid-Post 441 341 1658 3.427 0.795 0.191 0.065 9 1.2 G_cingul-Post-dorsal 264 192 942 3.236 1.025 0.163 0.050 5 0.5 G_cingul-Post-ventral 2319 1747 4274 2.025 0.622 0.182 0.063 52 6.1 G_cuneus 1358 1010 3549 2.540 0.747 0.169 0.061 27 4.4 G_front_inf-Opercular 458 339 1640 3.173 0.541 0.171 0.062 15 1.4 G_front_inf-Orbital 678 496 2438 3.087 0.673 0.152 0.044 16 1.3 G_front_inf-Triangul 5553 3883 18223 3.122 0.733 0.153 0.047 114 11.0 G_front_middle 7300 5365 22124 3.073 0.798 0.164 0.053 153 16.6 G_front_sup 843 509 1552 2.696 0.843 0.136 0.058 12 1.7 G_Ins_lg&S_cent_ins 763 491 2020 3.047 0.727 0.159 0.065 14 2.0 G_insular_short 2102 1479 5202 2.516 0.714 0.174 0.060 48 5.3 G_occipital_middle 1548 1117 3117 2.202 0.623 0.171 0.057 31 3.6 G_occipital_sup 1560 1150 3641 2.535 0.757 0.163 0.054 34 4.1 G_oc-temp_lat-fusifor 2746 2069 5787 2.141 0.754 0.188 0.070 66 8.2 G_oc-temp_med-Lingual 1700 1094 3667 2.648 0.965 0.136 0.055 30 3.7 G_oc-temp_med-Parahip 2602 1793 5997 2.430 0.804 0.162 0.077 129 8.4 G_orbital 1903 1420 5850 2.796 0.758 0.171 0.059 52 4.6 G_pariet_inf-Angular 3395 2367 7525 2.511 0.796 0.160 0.059 72 8.9 G_pariet_inf-Supramar 3625 2587 10171 2.799 0.730 0.151 0.041 64 6.1 G_parietal_sup 2306 1625 4406 2.128 0.846 0.150 0.048 36 4.8 G_postcentral 3083 2126 7672 2.726 0.925 0.149 0.048 51 6.3 G_precentral 2941 2233 8822 2.901 0.787 0.183 0.056 73 7.4 G_precuneus 807 591 2301 2.749 0.775 0.176 0.071 22 2.3 G_rectus 158 107 397 2.776 0.818 0.171 0.074 5 0.4 G_subcallosal 384 446 1439 2.986 0.681 0.204 0.047 9 0.7 G_temp_sup-G_T_transv 2056 1753 5844 2.634 1.056 0.186 0.070 50 6.8 G_temp_sup-Lateral 802 620 2437 2.861 1.068 0.148 0.046 12 1.5 G_temp_sup-Plan_polar 1071 786 2244 2.573 0.658 0.129 0.037 13 1.7 G_temp_sup-Plan_tempo 2163 1583 5161 2.606 0.843 0.159 0.055 45 5.8 G_temporal_inf 2715 1926 6874 2.588 0.891 0.172 0.062 70 7.5 G_temporal_middle 200 135 372 2.567 0.525 0.109 0.019 1 0.2 Lat_Fis-ant-Horizont 260 187 468 2.949 0.651 0.088 0.016 1 0.1 Lat_Fis-ant-Vertical 1399 967 2002 2.584 0.685 0.124 0.032 11 2.1 Lat_Fis-post 2021 1474 4038 2.133 0.681 0.184 0.071 49 5.9 Pole_occipital 1441 1024 4366 3.021 0.861 0.161 0.071 32 4.6 Pole_temporal 2413 1837 3424 2.035 0.670 0.142 0.046 36 4.9 S_calcarine 3143 2185 3773 1.959 0.525 0.119 0.026 24 3.7 S_central 1144 775 1793 2.471 0.463 0.095 0.015 6 0.8 S_cingul-Marginalis 519 342 849 2.822 0.568 0.099 0.024 3 0.5 S_circular_insula_ant 1182 921 1962 2.415 0.858 0.140 0.058 52 4.1 S_circular_insula_inf 1694 1163 2688 2.991 0.504 0.109 0.022 9 1.7 S_circular_insula_sup 905 652 1551 2.237 0.719 0.109 0.023 7 0.9 S_collat_transv_ant 371 256 580 2.514 0.605 0.138 0.042 4 0.6 S_collat_transv_post 1584 1082 2702 2.601 0.519 0.104 0.021 10 1.5 S_front_inf 1975 1335 3155 2.721 0.481 0.107 0.022 14 1.9 S_front_middle 2731 1928 5124 2.724 0.536 0.111 0.024 21 2.4 S_front_sup 326 222 469 2.510 0.554 0.124 0.022 2 0.4 S_interm_prim-Jensen 2608 1769 3862 2.370 0.493 0.114 0.026 20 3.0 S_intrapariet&P_trans 863 626 1305 2.063 0.539 0.141 0.036 10 1.3 S_oc_middle&Lunatus 1214 822 2013 2.365 0.607 0.116 0.027 10 1.3 S_oc_sup&transversal 872 592 1126 2.157 0.460 0.105 0.023 6 0.9 S_occipital_ant 1124 753 1467 2.015 0.651 0.111 0.040 15 2.2 S_oc-temp_lat 1439 1104 2746 2.367 0.670 0.131 0.035 18 2.0 S_oc-temp_med&Lingual 365 277 539 2.038 0.490 0.112 0.019 2 0.3 S_orbital_lateral 487 352 958 2.959 0.694 0.131 0.028 7 0.4 S_orbital_med-olfact 1278 901 2218 2.410 0.653 0.120 0.029 12 1.5 S_orbital-H_Shaped 2282 1574 3455 2.424 0.624 0.122 0.028 29 2.8 S_parieto_occipital 1287 766 1005 1.561 0.627 0.110 0.025 20 1.0 S_pericallosal 2793 1910 4580 2.546 0.677 0.129 0.028 27 3.2 S_postcentral 2188 1567 4079 2.683 0.568 0.105 0.023 16 2.0 S_precentral-inf-part 1362 917 2096 2.510 0.671 0.100 0.018 8 1.0 S_precentral-sup-part 518 367 964 2.778 0.752 0.121 0.022 5 0.5 S_suborbital 1196 822 1860 2.789 0.638 0.132 0.031 11 1.6 S_subparietal 1148 960 2322 2.785 0.761 0.142 0.028 11 1.6 S_temporal_inf 4852 3983 9873 2.503 0.679 0.135 0.030 54 6.7 S_temporal_sup 463 314 652 2.426 0.568 0.093 0.023 3 0.5 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050418 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 276809 Total vertex volume 274048 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1110 721 1951 2.316 0.753 0.171 0.086 37 4.3 G&S_frontomargin 1237 873 2452 2.155 0.735 0.145 0.050 18 2.6 G&S_occipital_inf 1411 976 3050 2.436 0.699 0.135 0.044 20 2.3 G&S_paracentral 1492 1019 3179 2.469 0.698 0.129 0.039 19 2.2 G&S_subcentral 1246 881 3477 2.882 0.670 0.166 0.049 29 2.3 G&S_transv_frontopol 3418 2400 7759 2.989 0.701 0.126 0.033 42 4.9 G&S_cingul-Ant 1468 993 3414 3.259 0.594 0.113 0.024 11 1.5 G&S_cingul-Mid-Ant 1416 1029 3479 2.932 0.717 0.143 0.041 21 2.2 G&S_cingul-Mid-Post 340 270 1460 3.568 0.622 0.199 0.074 9 1.0 G_cingul-Post-dorsal 312 199 869 3.118 1.102 0.162 0.091 10 1.5 G_cingul-Post-ventral 2076 1551 3778 2.066 0.511 0.185 0.060 42 5.9 G_cuneus 1245 938 3055 2.552 0.802 0.165 0.051 26 2.8 G_front_inf-Opercular 452 314 1467 3.091 0.545 0.182 0.097 15 1.9 G_front_inf-Orbital 895 609 2811 3.125 0.676 0.161 0.054 21 1.9 G_front_inf-Triangul 4407 3230 14105 2.993 0.772 0.177 0.061 109 12.4 G_front_middle 7414 5108 22063 3.239 0.727 0.150 0.046 120 13.3 G_front_sup 641 471 1848 3.243 1.189 0.145 0.053 8 1.3 G_Ins_lg&S_cent_ins 542 365 1938 3.424 0.905 0.143 0.052 9 1.0 G_insular_short 2859 2000 7431 2.538 0.731 0.168 0.061 66 8.0 G_occipital_middle 1301 895 2965 2.425 0.657 0.140 0.038 20 2.0 G_occipital_sup 1856 1389 4417 2.354 0.792 0.163 0.052 35 4.4 G_oc-temp_lat-fusifor 2042 1597 5367 2.580 0.701 0.180 0.058 43 4.8 G_oc-temp_med-Lingual 929 682 2729 2.774 0.855 0.159 0.059 17 1.8 G_oc-temp_med-Parahip 3353 2202 8101 2.560 0.916 0.163 0.072 77 10.4 G_orbital 2257 1670 7036 3.009 0.787 0.174 0.059 54 5.8 G_pariet_inf-Angular 3095 2184 8079 2.757 0.684 0.158 0.053 61 6.7 G_pariet_inf-Supramar 3415 2489 9315 2.731 0.759 0.166 0.050 76 7.7 G_parietal_sup 2050 1371 3129 1.900 0.548 0.141 0.049 33 4.1 G_postcentral 3360 2214 8546 2.824 0.856 0.146 0.062 64 9.6 G_precentral 2696 1943 7097 2.827 0.639 0.176 0.062 66 7.9 G_precuneus 833 546 2339 3.065 0.819 0.155 0.053 16 2.0 G_rectus 589 380 942 2.522 1.223 0.101 0.058 7 1.1 G_subcallosal 436 291 975 2.807 0.784 0.154 0.052 9 0.9 G_temp_sup-G_T_transv 1880 1316 4796 2.765 0.793 0.156 0.062 37 5.0 G_temp_sup-Lateral 646 558 1911 2.862 0.930 0.156 0.046 11 1.2 G_temp_sup-Plan_polar 793 573 1509 2.449 0.531 0.109 0.025 7 0.8 G_temp_sup-Plan_tempo 2137 1568 6347 2.822 0.854 0.165 0.068 54 6.2 G_temporal_inf 2864 1878 9003 3.277 0.739 0.140 0.054 57 6.2 G_temporal_middle 334 239 548 2.405 0.636 0.096 0.017 1 0.2 Lat_Fis-ant-Horizont 345 226 482 2.469 0.646 0.097 0.024 1 0.3 Lat_Fis-ant-Vertical 1350 886 2011 2.787 0.820 0.105 0.021 8 1.2 Lat_Fis-post 3095 2289 7119 2.367 0.690 0.173 0.067 61 8.5 Pole_occipital 1356 1128 3812 2.512 0.776 0.183 0.066 29 3.9 Pole_temporal 2021 1440 3074 2.477 0.667 0.135 0.035 24 2.8 S_calcarine 2865 1921 3574 2.013 0.647 0.097 0.018 17 2.0 S_central 1103 774 1586 2.373 0.711 0.118 0.023 8 1.1 S_cingul-Marginalis 571 378 1066 3.089 0.666 0.109 0.026 3 0.6 S_circular_insula_ant 766 791 2005 2.684 0.971 0.112 0.021 4 0.7 S_circular_insula_inf 1137 793 2078 2.895 0.668 0.109 0.025 7 1.2 S_circular_insula_sup 833 608 1280 2.148 0.571 0.113 0.024 6 1.0 S_collat_transv_ant 426 304 505 2.089 0.567 0.135 0.033 4 0.7 S_collat_transv_post 1823 1313 3757 2.825 0.693 0.116 0.025 14 2.1 S_front_inf 2327 1634 3987 2.629 0.553 0.123 0.032 21 3.0 S_front_middle 2452 1712 5003 2.814 0.632 0.108 0.023 16 2.2 S_front_sup 559 407 1034 2.988 0.584 0.134 0.027 5 0.7 S_interm_prim-Jensen 3225 2215 5373 2.395 0.512 0.107 0.023 20 3.0 S_intrapariet&P_trans 975 682 1236 1.993 0.461 0.120 0.030 7 1.3 S_oc_middle&Lunatus 1104 728 1419 1.987 0.447 0.118 0.029 9 1.3 S_oc_sup&transversal 728 506 982 2.016 0.531 0.125 0.037 9 1.4 S_occipital_ant 506 385 1144 2.463 0.821 0.120 0.030 4 0.5 S_oc-temp_lat 1523 1045 2457 2.151 0.639 0.119 0.036 18 2.4 S_oc-temp_med&Lingual 566 403 957 2.657 0.736 0.108 0.024 3 0.5 S_orbital_lateral 469 330 782 2.563 0.682 0.128 0.027 4 0.5 S_orbital_med-olfact 1521 1042 2657 2.611 0.730 0.129 0.039 16 2.4 S_orbital-H_Shaped 2454 1657 3657 2.439 0.695 0.127 0.030 27 3.1 S_parieto_occipital 1321 875 1821 2.232 0.912 0.125 0.021 17 0.9 S_pericallosal 2743 1856 3917 2.241 0.536 0.112 0.025 21 2.6 S_postcentral 1553 1048 2890 2.859 0.485 0.109 0.020 11 1.2 S_precentral-inf-part 1601 1112 2575 2.793 0.491 0.104 0.021 8 1.5 S_precentral-sup-part 330 228 520 2.935 0.900 0.136 0.024 3 0.3 S_suborbital 1049 754 1966 2.618 0.578 0.148 0.042 16 1.8 S_subparietal 1224 875 2003 2.679 0.654 0.120 0.036 11 2.3 S_temporal_inf 5721 3988 10146 2.516 0.726 0.115 0.029 52 7.1 S_temporal_sup 221 181 436 3.027 0.675 0.149 0.019 2 0.2 S_temporal_transverse PIDs (5664 5667) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 29 08:36:10 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Sun Oct 29 08:36:10 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 5757 of (5757 5760) to complete... Waiting for PID 5760 of (5757 5760) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1006 labels changed using aseg relabeling using gibbs priors... 000: 1922 changed, 131248 examined... 001: 434 changed, 9152 examined... 002: 126 changed, 2545 examined... 003: 48 changed, 724 examined... 004: 21 changed, 270 examined... 005: 12 changed, 120 examined... 006: 10 changed, 73 examined... 007: 7 changed, 56 examined... 008: 6 changed, 38 examined... 009: 5 changed, 33 examined... 010: 6 changed, 24 examined... 011: 2 changed, 30 examined... 012: 3 changed, 12 examined... 013: 1 changed, 17 examined... 014: 2 changed, 11 examined... 015: 2 changed, 14 examined... 016: 1 changed, 12 examined... 017: 0 changed, 7 examined... 109 labels changed using aseg 000: 71 total segments, 38 labels (395 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 812 vertices marked for relabeling... 812 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 26 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050418 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1154 labels changed using aseg relabeling using gibbs priors... 000: 1939 changed, 129560 examined... 001: 446 changed, 9005 examined... 002: 114 changed, 2442 examined... 003: 41 changed, 695 examined... 004: 17 changed, 261 examined... 005: 11 changed, 110 examined... 006: 5 changed, 69 examined... 007: 1 changed, 35 examined... 008: 0 changed, 6 examined... 86 labels changed using aseg 000: 60 total segments, 27 labels (182 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 839 vertices marked for relabeling... 839 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 26 seconds. PIDs (5757 5760) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 29 08:36:36 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050418 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 29 08:36:36 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050418 rh white Waiting for PID 5818 of (5818 5821) to complete... Waiting for PID 5821 of (5818 5821) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050418 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 275133 Total vertex volume 271693 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1779 1216 3660 2.561 0.793 0.127 0.033 23 2.4 caudalanteriorcingulate 3588 2482 8548 2.875 0.717 0.116 0.025 34 3.4 caudalmiddlefrontal 3483 2561 5985 2.112 0.572 0.165 0.052 65 7.7 cuneus 716 441 1581 2.646 0.964 0.153 0.070 17 2.1 entorhinal 3584 2637 7251 2.354 0.738 0.146 0.047 62 7.7 fusiform 5453 3985 12607 2.572 0.699 0.144 0.042 92 9.6 inferiorparietal 4233 3140 9513 2.576 0.854 0.145 0.049 74 10.3 inferiortemporal 1356 938 3063 2.551 1.107 0.140 0.043 21 2.2 isthmuscingulate 6627 4814 14102 2.318 0.707 0.165 0.054 127 14.7 lateraloccipital 4475 3011 9057 2.500 0.811 0.147 0.060 150 11.1 lateralorbitofrontal 3821 2867 7323 2.150 0.710 0.165 0.057 73 9.2 lingual 1649 1201 4032 2.760 0.757 0.155 0.050 32 3.4 medialorbitofrontal 5828 4414 12860 2.559 0.806 0.153 0.046 102 11.7 middletemporal 1086 719 2259 2.589 0.930 0.120 0.040 14 1.7 parahippocampal 2460 1749 4943 2.549 0.685 0.136 0.040 56 4.4 paracentral 1809 1369 4474 2.854 0.658 0.152 0.046 30 4.3 parsopercularis 770 608 2287 2.870 0.663 0.135 0.041 9 1.3 parsorbitalis 1684 1183 4205 2.841 0.620 0.127 0.035 29 2.7 parstriangularis 1947 1406 2476 1.858 0.622 0.154 0.054 34 4.7 pericalcarine 7680 5343 12883 2.231 0.804 0.138 0.041 100 13.5 postcentral 1679 1222 3703 2.749 0.826 0.132 0.028 22 1.9 posteriorcingulate 8598 5865 16339 2.481 0.786 0.134 0.040 105 15.1 precentral 5946 4323 13654 2.764 0.724 0.154 0.043 108 11.4 precuneus 1396 977 3736 3.037 0.930 0.149 0.044 22 2.7 rostralanteriorcingulate 6266 4343 14968 2.772 0.668 0.134 0.039 103 10.4 rostralmiddlefrontal 12749 9153 34311 2.989 0.737 0.144 0.042 208 23.1 superiorfrontal 6704 4674 14979 2.582 0.681 0.140 0.037 93 10.2 superiorparietal 7644 6140 18475 2.616 0.911 0.154 0.052 168 19.2 superiortemporal 5649 3970 11420 2.615 0.754 0.145 0.046 92 11.3 supramarginal 474 444 1334 2.688 0.628 0.172 0.047 7 0.8 transversetemporal 2838 1905 5664 2.881 0.682 0.130 0.040 29 4.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 0050418 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 276809 Total vertex volume 274048 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1154 776 3069 3.135 1.025 0.126 0.028 13 1.4 caudalanteriorcingulate 3397 2407 8842 3.106 0.644 0.129 0.031 37 4.6 caudalmiddlefrontal 2794 2027 4733 2.120 0.515 0.160 0.049 44 6.5 cuneus 323 267 1288 3.059 0.941 0.151 0.039 3 0.4 entorhinal 3527 2571 7293 2.243 0.741 0.151 0.048 60 7.4 fusiform 6864 4953 15517 2.545 0.797 0.149 0.043 113 13.1 inferiorparietal 4191 3094 10000 2.595 0.833 0.147 0.055 78 9.9 inferiortemporal 1139 782 2763 2.770 0.980 0.153 0.047 24 1.9 isthmuscingulate 7288 5155 15142 2.307 0.669 0.157 0.054 124 17.1 lateraloccipital 4687 3060 8911 2.447 0.859 0.154 0.066 92 13.6 lateralorbitofrontal 3227 2496 7377 2.495 0.692 0.162 0.051 55 6.6 lingual 1971 1323 4447 2.927 0.978 0.129 0.040 26 2.9 medialorbitofrontal 5756 3901 14442 2.960 0.798 0.127 0.043 83 10.8 middletemporal 856 596 1878 2.546 0.745 0.126 0.045 12 1.3 parahippocampal 2036 1438 4261 2.614 0.671 0.125 0.031 22 2.5 paracentral 2096 1491 4320 2.693 0.693 0.132 0.036 31 3.1 parsopercularis 1257 857 3035 2.836 0.665 0.162 0.073 28 4.1 parsorbitalis 2035 1438 5113 2.889 0.696 0.132 0.037 27 2.7 parstriangularis 1794 1277 2889 2.265 0.648 0.152 0.050 26 3.3 pericalcarine 6572 4404 9736 1.982 0.610 0.120 0.033 73 8.6 postcentral 1695 1267 4304 2.916 0.854 0.158 0.042 29 2.9 posteriorcingulate 7467 4986 15449 2.687 0.743 0.125 0.042 93 13.9 precentral 5902 4154 12093 2.669 0.694 0.153 0.048 106 13.1 precuneus 1374 955 3499 3.071 0.828 0.135 0.044 24 2.4 rostralanteriorcingulate 6201 4485 14936 2.681 0.718 0.152 0.051 116 14.3 rostralmiddlefrontal 14837 10276 37644 3.045 0.701 0.139 0.039 212 22.9 superiorfrontal 7316 5113 16307 2.540 0.680 0.139 0.038 113 12.4 superiorparietal 6205 4696 14319 2.656 0.760 0.137 0.043 85 11.4 superiortemporal 5577 3941 12659 2.789 0.680 0.139 0.040 79 8.9 supramarginal 469 312 901 2.634 0.656 0.158 0.054 10 1.0 transversetemporal 2703 1951 6880 3.116 0.969 0.121 0.035 26 3.8 insula PIDs (5818 5821) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 29 08:37:44 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts pctsurfcon --s 0050418 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 29 08:37:44 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts pctsurfcon --s 0050418 --rh-only Waiting for PID 5991 of (5991 5994) to complete... Waiting for PID 5994 of (5991 5994) to complete... pctsurfcon --s 0050418 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts/pctsurfcon.log Sun Oct 29 08:37:44 CET 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux tars-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.wm.mgh --regheader 0050418 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 62946 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.wm.mgh Dim: 131248 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.gm.mgh --projfrac 0.3 --regheader 0050418 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 75606 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.gm.mgh Dim: 131248 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5991/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.w-g.pct.mgh --annot 0050418 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.w-g.pct.mgh --annot 0050418 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-623 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.w-g.pct.mgh Vertex Area is 0.713875 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s 0050418 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts/pctsurfcon.log Sun Oct 29 08:37:44 CET 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/scripts /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux tars-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.wm.mgh --regheader 0050418 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 62076 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.wm.mgh Dim: 129560 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.gm.mgh --projfrac 0.3 --regheader 0050418 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 74786 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.gm.mgh Dim: 129560 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/tmp.pctsurfcon.5994/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.w-g.pct.mgh --annot 0050418 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.w-g.pct.mgh --annot 0050418 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-623 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.w-g.pct.mgh Vertex Area is 0.703019 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (5991 5994) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 29 08:37:55 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3159 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1930 voxels changed to hypointensity... 5601 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 29 08:38:16 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_aparc2aseg --s 0050418 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Sun Oct 29 08:38:16 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_aparc2aseg --s 0050418 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sun Oct 29 08:38:16 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_aparc2aseg --s 0050418 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Waiting for PID 6141 of (6141 6144 6147) to complete... Waiting for PID 6144 of (6141 6144 6147) to complete... Waiting for PID 6147 of (6141 6144 6147) to complete... mri_aparc2aseg --s 0050418 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050418 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.98 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 62 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 83 rescaling Left_Cerebellum_Cortex from 60 --> 53 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 67 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 16 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 81 rescaling Left_Hippocampus from 57 --> 58 rescaling Left_Amygdala from 56 --> 60 rescaling CSF from 32 --> 22 rescaling Left_Accumbens_area from 62 --> 60 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 64 rescaling Right_Lateral_Ventricle from 13 --> 9 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 61 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 19 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 538226 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 100 changed. pass 2: 9 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050418 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050418 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.98 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 62 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 83 rescaling Left_Cerebellum_Cortex from 60 --> 53 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 67 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 16 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 81 rescaling Left_Hippocampus from 57 --> 58 rescaling Left_Amygdala from 56 --> 60 rescaling CSF from 32 --> 22 rescaling Left_Accumbens_area from 62 --> 60 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 64 rescaling Right_Lateral_Ventricle from 13 --> 9 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 61 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 19 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 538261 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 100 changed. pass 2: 9 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050418 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050418 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.98 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 62 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 83 rescaling Left_Cerebellum_Cortex from 60 --> 53 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 67 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 93 rescaling Third_Ventricle from 25 --> 16 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 81 rescaling Left_Hippocampus from 57 --> 58 rescaling Left_Amygdala from 56 --> 60 rescaling CSF from 32 --> 22 rescaling Left_Accumbens_area from 62 --> 60 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 64 rescaling Right_Lateral_Ventricle from 13 --> 9 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 61 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 19 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 538261 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 100 changed. pass 2: 9 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (6141 6144 6147) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 29 08:53:37 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 29 08:53:37 CET 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux tars-623 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname tars-623 machine x86_64 user ntraut input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Sun Oct 29 08:53:37 CET 2017 Ended at Sun Oct 29 08:53:44 CET 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 29 08:53:44 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0050418 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0050418 sysname Linux hostname tars-623 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) Computing euler number orig.nofix lheno = -514, rheno = -316 orig.nofix lhholes = 258, rhholes = 159 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Sun Oct 29 08:56:44 CET 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418 mri_aparc2aseg --s 0050418 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050418 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7273 vertices from left hemi Ripped 6896 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 951163 Used brute-force search on 163 voxels Fixing Parahip LH WM Found 7 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1478.000000 5 k 2.000000 6 k 14.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1096.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 49.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050418 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050418 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-623 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 29 09:05:49 CET 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 7625 of (7625 7628 7631 7639 7649) to complete... Waiting for PID 7628 of (7625 7628 7631 7639 7649) to complete... Waiting for PID 7631 of (7625 7628 7631 7639 7649) to complete... Waiting for PID 7639 of (7625 7628 7631 7639 7649) to complete... Waiting for PID 7649 of (7625 7628 7631 7639 7649) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 361 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4490 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 663 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4338 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 692 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6675 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 582 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6366 mri_label2label: Done PIDs (7625 7628 7631 7639 7649) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 7706 of (7706 7712 7718 7724) to complete... Waiting for PID 7712 of (7706 7712 7718 7724) to complete... Waiting for PID 7718 of (7706 7712 7718 7724) to complete... Waiting for PID 7724 of (7706 7712 7718 7724) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4318 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 1493 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15082 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 664 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4845 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050418 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 336 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3758 mri_label2label: Done PIDs (7706 7712 7718 7724) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0050418 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0050418 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050418 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0050418 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0050418 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 7762 of (7762 7768 7774 7780 7784) to complete... Waiting for PID 7768 of (7762 7768 7774 7780 7784) to complete... Waiting for PID 7774 of (7762 7768 7774 7780 7784) to complete... Waiting for PID 7780 of (7762 7768 7774 7780 7784) to complete... Waiting for PID 7784 of (7762 7768 7774 7780 7784) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0050418 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 1380 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6021 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0050418 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 2606 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10720 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050418 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 417 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2435 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0050418 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 250 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1540 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0050418 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 229 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1428 mri_label2label: Done PIDs (7762 7768 7774 7780 7784) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 7838 of (7838 7844 7850 7856 7861) to complete... Waiting for PID 7844 of (7838 7844 7850 7856 7861) to complete... Waiting for PID 7850 of (7838 7844 7850 7856 7861) to complete... Waiting for PID 7856 of (7838 7844 7850 7856 7861) to complete... Waiting for PID 7861 of (7838 7844 7850 7856 7861) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2181 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1567 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2098 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 233 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2552 mri_label2label: Done PIDs (7838 7844 7850 7856 7861) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 7921 of (7921 7927 7933 7939) to complete... Waiting for PID 7927 of (7921 7927 7933 7939) to complete... Waiting for PID 7933 of (7921 7927 7933 7939) to complete... Waiting for PID 7939 of (7921 7927 7933 7939) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1626 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 592 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 201 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2113 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1263 mri_label2label: Done PIDs (7921 7927 7933 7939) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 7992 of (7992 7998 8004 8010 8016) to complete... Waiting for PID 7998 of (7992 7998 8004 8010 8016) to complete... Waiting for PID 8004 of (7992 7998 8004 8010 8016) to complete... Waiting for PID 8010 of (7992 7998 8004 8010 8016) to complete... Waiting for PID 8016 of (7992 7998 8004 8010 8016) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 950 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4355 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 1172 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4506 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 619 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 131248 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 563 mri_label2label: Done PIDs (7992 7998 8004 8010 8016) completed and logs appended. mris_label2annot --s 0050418 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label cmdline mris_label2annot --s 0050418 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname tars-623 machine x86_64 user ntraut subject 0050418 hemi lh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 90918 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.BA_exvivo.annot mris_label2annot --s 0050418 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label cmdline mris_label2annot --s 0050418 --hemi lh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname tars-623 machine x86_64 user ntraut subject 0050418 hemi lh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 108003 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 0050418 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 275133 Total vertex volume 271693 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 1107 783 2058 2.064 0.745 0.167 0.057 23 2.8 BA1_exvivo 3776 2614 6883 2.473 0.718 0.133 0.036 44 5.6 BA2_exvivo 1133 718 1108 1.993 0.407 0.146 0.042 36 2.1 BA3a_exvivo 2747 1840 3374 1.745 0.564 0.127 0.041 33 5.0 BA3b_exvivo 1781 1234 3112 2.276 0.603 0.145 0.045 25 3.6 BA4a_exvivo 1289 926 1880 2.127 0.556 0.122 0.031 9 2.0 BA4p_exvivo 9463 6696 24724 2.974 0.832 0.137 0.040 130 15.7 BA6_exvivo 2399 1750 5664 2.692 0.690 0.140 0.041 34 4.6 BA44_exvivo 2191 1619 6224 2.880 0.656 0.147 0.043 50 4.3 BA45_exvivo 3382 2521 5167 1.893 0.627 0.166 0.061 66 8.7 V1_exvivo 7637 5665 14638 2.178 0.677 0.176 0.062 162 19.9 V2_exvivo 1940 1438 4375 2.455 0.629 0.142 0.040 29 2.9 MT_exvivo 710 416 1457 2.618 0.924 0.127 0.054 13 1.5 perirhinal_exvivo 775 552 2057 2.925 1.045 0.144 0.048 13 1.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050418 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 275133 Total vertex volume 271693 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 685 466 1343 2.115 0.768 0.191 0.073 17 2.1 BA1_exvivo 1356 974 2875 2.506 0.812 0.129 0.032 15 1.7 BA2_exvivo 908 584 885 2.029 0.381 0.155 0.044 33 1.8 BA3a_exvivo 1396 1036 1734 1.565 0.369 0.099 0.020 9 1.1 BA3b_exvivo 1702 1193 3108 2.355 0.594 0.134 0.036 17 2.8 BA4a_exvivo 1048 758 1461 2.117 0.551 0.120 0.030 7 1.5 BA4p_exvivo 5094 3558 13107 2.960 0.877 0.142 0.043 72 8.8 BA6_exvivo 1392 1060 3398 2.680 0.663 0.144 0.044 23 3.2 BA44_exvivo 889 678 2888 3.032 0.676 0.164 0.042 19 1.9 BA45_exvivo 3575 2666 5483 1.886 0.614 0.167 0.063 70 9.9 V1_exvivo 3866 2949 7436 2.113 0.692 0.186 0.065 91 10.9 V2_exvivo 527 361 874 2.401 0.599 0.141 0.043 9 0.9 MT_exvivo 355 226 764 2.353 0.826 0.109 0.050 5 0.7 perirhinal_exvivo 452 321 1013 2.840 1.129 0.141 0.057 8 1.0 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 29 09:10:34 CET 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 8123 of (8123 8129 8135 8141 8147) to complete... Waiting for PID 8129 of (8123 8129 8135 8141 8147) to complete... Waiting for PID 8135 of (8123 8129 8135 8141 8147) to complete... Waiting for PID 8141 of (8123 8129 8135 8141 8147) to complete... Waiting for PID 8147 of (8123 8129 8135 8141 8147) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 373 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 416 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7103 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4095 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 243 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 405 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6152 mri_label2label: Done PIDs (8123 8129 8135 8141 8147) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 8203 of (8203 8209 8215 8221) to complete... Waiting for PID 8209 of (8203 8209 8215 8221) to complete... Waiting for PID 8215 of (8203 8209 8215 8221) to complete... Waiting for PID 8221 of (8203 8209 8215 8221) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 259 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4732 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 1657 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13913 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 743 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7655 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050418 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 1027 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6382 mri_label2label: Done PIDs (8203 8209 8215 8221) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0050418 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050418 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0050418 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0050418 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0050418 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 8288 of (8288 8294 8300 8306 8312) to complete... Waiting for PID 8294 of (8288 8294 8300 8306 8312) to complete... Waiting for PID 8300 of (8288 8294 8300 8306 8312) to complete... Waiting for PID 8306 of (8288 8294 8300 8306 8312) to complete... Waiting for PID 8312 of (8288 8294 8300 8306 8312) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0050418 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 1254 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5981 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050418 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 1989 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10005 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0050418 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 793 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2725 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0050418 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1142 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0050418 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 862 mri_label2label: Done PIDs (8288 8294 8300 8306 8312) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 8371 of (8371 8377 8383 8389 8393) to complete... Waiting for PID 8377 of (8371 8377 8383 8389 8393) to complete... Waiting for PID 8383 of (8371 8377 8383 8389 8393) to complete... Waiting for PID 8389 of (8371 8377 8383 8389 8393) to complete... Waiting for PID 8393 of (8371 8377 8383 8389 8393) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 987 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2817 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1740 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2282 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1415 mri_label2label: Done PIDs (8371 8377 8383 8389 8393) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 8432 of (8432 8438 8444 8450) to complete... Waiting for PID 8438 of (8432 8438 8444 8450) to complete... Waiting for PID 8444 of (8432 8438 8444 8450) to complete... Waiting for PID 8450 of (8432 8438 8444 8450) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1612 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 791 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7750 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1164 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1383 mri_label2label: Done PIDs (8432 8438 8444 8450) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 8517 of (8517 8523 8529 8535 8539) to complete... Waiting for PID 8523 of (8517 8523 8529 8535 8539) to complete... Waiting for PID 8529 of (8517 8523 8529 8535 8539) to complete... Waiting for PID 8535 of (8517 8523 8529 8535 8539) to complete... Waiting for PID 8539 of (8517 8523 8529 8535 8539) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 788 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4020 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 941 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4378 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 407 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 729 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0050418 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050418 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 129560 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 314 mri_label2label: Done PIDs (8517 8523 8529 8535 8539) completed and logs appended. mris_label2annot --s 0050418 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label cmdline mris_label2annot --s 0050418 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname tars-623 machine x86_64 user ntraut subject 0050418 hemi rh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 90399 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.BA_exvivo.annot mris_label2annot --s 0050418 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label cmdline mris_label2annot --s 0050418 --hemi rh --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname tars-623 machine x86_64 user ntraut subject 0050418 hemi rh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 108204 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 0050418 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 276809 Total vertex volume 274048 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 965 594 1442 1.907 0.542 0.152 0.061 18 2.5 BA1_exvivo 3051 2069 4420 2.142 0.559 0.119 0.031 31 3.6 BA2_exvivo 1074 702 1119 1.934 0.510 0.128 0.025 10 1.0 BA3a_exvivo 1836 1273 2559 1.741 0.573 0.101 0.029 15 2.0 BA3b_exvivo 1267 924 2915 2.686 0.660 0.126 0.040 11 2.0 BA4a_exvivo 1167 788 1877 2.392 0.588 0.103 0.027 14 1.3 BA4p_exvivo 8952 6098 22173 2.979 0.707 0.130 0.040 108 15.6 BA6_exvivo 3402 2382 7151 2.782 0.694 0.128 0.035 44 5.0 BA44_exvivo 4042 2802 10192 2.826 0.716 0.141 0.049 67 8.1 BA45_exvivo 3305 2506 6812 2.307 0.663 0.170 0.060 58 8.3 V1_exvivo 6828 4981 13845 2.357 0.680 0.166 0.053 122 15.4 V2_exvivo 2434 1770 4704 2.242 0.620 0.156 0.050 46 5.9 MT_exvivo 459 363 1805 3.165 0.913 0.152 0.043 6 0.7 perirhinal_exvivo 379 265 838 2.486 0.694 0.173 0.064 8 1.0 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050418 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050418/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 276809 Total vertex volume 274048 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1574874 mm^3 (det: 1.236991 ) lhCtxGM: 269017.890 269026.000 diff= -8.1 pctdiff=-0.003 rhCtxGM: 270588.895 270359.000 diff= 229.9 pctdiff= 0.085 lhCtxWM: 206072.430 206920.000 diff= -847.6 pctdiff=-0.411 rhCtxWM: 206417.922 207270.000 diff= -852.1 pctdiff=-0.413 SubCortGMVol 59871.000 SupraTentVol 1023294.138 (1021093.000) diff=2201.138 pctdiff=0.215 SupraTentVolNotVent 1015664.138 (1013463.000) diff=2201.138 pctdiff=0.217 BrainSegVol 1174218.000 (1172016.000) diff=2202.000 pctdiff=0.188 BrainSegVolNotVent 1163718.000 (1162156.138) diff=1561.862 pctdiff=0.134 BrainSegVolNotVent 1163718.000 CerebellumVol 150171.000 VentChorVol 7630.000 3rd4th5thCSF 2870.000 CSFVol 668.000, OptChiasmVol 84.000 MaskVol 1524796.000 645 403 939 1.880 0.522 0.166 0.063 13 1.9 BA1_exvivo 1656 1129 2328 1.977 0.516 0.107 0.027 14 1.7 BA2_exvivo 949 615 921 1.929 0.480 0.128 0.023 9 0.9 BA3a_exvivo 1409 1002 1735 1.573 0.476 0.088 0.021 8 1.2 BA3b_exvivo 721 516 1820 2.880 0.559 0.121 0.032 7 0.9 BA4a_exvivo 1025 679 1567 2.394 0.612 0.101 0.027 13 1.2 BA4p_exvivo 5444 3728 13486 2.942 0.698 0.127 0.039 62 9.1 BA6_exvivo 822 653 1808 2.392 0.735 0.167 0.047 18 1.7 BA44_exvivo 1025 714 2888 2.895 0.711 0.152 0.051 21 1.8 BA45_exvivo 3157 2380 6310 2.314 0.659 0.169 0.060 54 8.0 V1_exvivo 3658 2700 8094 2.405 0.713 0.171 0.053 69 8.0 V2_exvivo 383 249 998 2.673 0.606 0.153 0.064 9 1.1 MT_exvivo 253 201 1055 3.172 0.994 0.127 0.036 2 0.3 perirhinal_exvivo 209 175 622 2.816 0.667 0.166 0.047 3 0.4 entorhinal_exvivo Started at Thu Oct 26 21:16:50 CEST 2017 Ended at Sun Oct 29 09:15:14 CET 2017 #@#%# recon-all-run-time-hours 60.973 recon-all -s 0050418 finished without error at Sun Oct 29 09:15:14 CET 2017