Sat Oct 7 17:43:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0051105 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051105/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0051105 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-967 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: 66074836 46479388 19595448 1741576 0 41844320 -/+ buffers/cache: 4635068 61439768 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: 2017/10/07-15:43:51-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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: 2017/10/07-15:43:52-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-967 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-6.0.0/0051105 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051105/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/NYU/0051105/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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/NYU/0051105/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-6.0.0/0051105/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 17:43:54 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 17:44:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-967 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 Sat Oct 7 17:44:04 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.27250 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27250/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27250/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.27250/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:44:06 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.27250/nu0.mnc ./tmp.mri_nu_correct.mni.27250/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27250/0/ -iterations 1000 -distance 50 [ntraut@tars-967:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/] [2017-10-07 17:44:06] 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.27250/0/ ./tmp.mri_nu_correct.mni.27250/nu0.mnc ./tmp.mri_nu_correct.mni.27250/nu1.imp 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Processing:.................................................................Done Number of iterations: 49 CV of field change: 0.000983605 mri_convert ./tmp.mri_nu_correct.mni.27250/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.27250/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.27250/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... Sat Oct 7 17:45:21 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 Sat Oct 7 17:45:21 CEST 2017 Ended at Sat Oct 7 17:45:59 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 17:46:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5587, pval=0.2115 >= 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-6.0.0/0051105/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/talairach_avi.log TalAviQA: 0.97790 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 17:46:02 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-6.0.0/0051105/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-967 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 Sat Oct 7 17:46:02 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.28125 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28125/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28125/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.28125/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 17:46:04 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.28125/nu0.mnc ./tmp.mri_nu_correct.mni.28125/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28125/0/ [ntraut@tars-967:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/] [2017-10-07 17:46:04] 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.28125/0/ ./tmp.mri_nu_correct.mni.28125/nu0.mnc ./tmp.mri_nu_correct.mni.28125/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.000947781 -------------------------------------------------------- Iteration 2 Sat Oct 7 17:46:58 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.28125/nu1.mnc ./tmp.mri_nu_correct.mni.28125/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.28125/1/ [ntraut@tars-967:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/] [2017-10-07 17:46:58] 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.28125/1/ ./tmp.mri_nu_correct.mni.28125/nu1.mnc ./tmp.mri_nu_correct.mni.28125/nu2.imp Processing:.................................................................Done 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of field change: 0.000985244 mri_binarize --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28125/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-6.0.0/0051105/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28125/ones.mgz sysname Linux hostname tars-967 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.28125/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.28125/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.28125/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/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.28125/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/input.mean.dat sysname Linux hostname tars-967 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28125/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.28125/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28125/ones.mgz --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/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.28125/ones.mgz --i ./tmp.mri_nu_correct.mni.28125/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28125/output.mean.dat sysname Linux hostname tars-967 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28125/ones.mgz Loading ./tmp.mri_nu_correct.mni.28125/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.28125/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.28125/nu2.mnc ./tmp.mri_nu_correct.mni.28125/nu2.mnc mul .95629133082067140491 Saving result to './tmp.mri_nu_correct.mni.28125/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.28125/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.28125/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.28125/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 8 seconds. mapping ( 9, 152) to ( 3, 110) Sat Oct 7 17:48:14 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 17:48:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 1.05304 -0.01733 -0.04726 -2.73104; 0.01785 1.01882 0.45608 -13.62891; 0.04319 -0.46862 1.08004 -16.75069; 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 = 16 Starting OpenSpline(): npoints = 16 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 109 gm peak at 64 (64), valley at 25 (25) csf peak at 32, setting threshold to 53 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 25 (25) 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 4 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 17:50:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 2 == 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=7.0 skull bounding box = (41, 35, 26) --> (206, 189, 220) using (96, 86, 123) as brain centroid... mean wm in atlas = 108, using box (76,67,99) --> (116, 104,146) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 5.5 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.349 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.351659 @ (0.000, 0.000, 0.000) max log p = -4.236966 @ (4.545, 4.545, -13.636) max log p = -4.194746 @ (-2.273, 6.818, -6.818) max log p = -4.160437 @ (-1.136, -7.955, 3.409) max log p = -4.160437 @ (0.000, 0.000, 0.000) max log p = -4.160437 @ (0.000, 0.000, 0.000) Found translation: (1.1, 3.4, -17.0): log p = -4.160 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.759, old_max_log_p =-4.160 (thresh=-4.2) 1.06375 0.00000 0.00000 -6.75199; 0.00000 1.14215 0.47309 -60.86976; 0.00000 -0.44009 1.06246 34.07212; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.759, old_max_log_p =-3.759 (thresh=-3.8) 1.06375 0.00000 0.00000 -6.75199; 0.00000 1.14215 0.47309 -60.86976; 0.00000 -0.44009 1.06246 34.07212; 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=-3.637, old_max_log_p =-3.759 (thresh=-3.8) 1.06244 -0.05118 0.02491 -3.48107; 0.02985 1.11097 0.42465 -58.21355; -0.03378 -0.38228 1.01610 38.65500; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.637 (thresh=-3.6) 1.04252 -0.05022 0.02444 -1.07439; 0.02926 1.11846 0.46625 -62.39538; -0.03473 -0.41842 1.00166 45.25020; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.633, old_max_log_p =-3.633 (thresh=-3.6) 1.04252 -0.05022 0.02444 -1.07439; 0.02926 1.11846 0.46625 -62.39538; -0.03473 -0.41842 1.00166 45.25020; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.617, old_max_log_p =-3.633 (thresh=-3.6) 1.04426 -0.05690 0.04105 -2.48448; 0.02976 1.12252 0.44874 -61.75409; -0.05124 -0.39872 1.00744 43.12392; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.617, old_max_log_p =-3.617 (thresh=-3.6) 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 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 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.617 (old=-4.349) transform before final EM align: 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 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 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.1 tol 0.000000 final transform: 1.04569 -0.04779 0.04484 -4.30427; 0.02082 1.12096 0.45715 -61.02280; -0.05142 -0.40741 1.00256 44.87205; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1264.968695 mri_em_register stimesec 1.334797 mri_em_register ru_maxrss 609824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157572 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 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 81 mri_em_register ru_nivcsw 3655 registration took 11 minutes and 3 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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=123 y=104 z=117 r=68 first estimation of the main basin volume: 1373919 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=147, y=101, z=84, Imax=255 CSF=12, 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=9366995510 voxels, voxel volume =1.000 = 9366995510 mmm3 = 9366995.968 cm3 done. PostAnalyze...Basin Prior 137 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=124,y=113, z=111, r=9455 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 43407 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1033560618 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1051113528 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 1080018188 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 1067824956 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=36 , nb = 1080265950 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 35, 35, 35, 56 after analyzing : 27, 35, 35, 40 RIGHT_CER before analyzing : 20, 26, 36, 62 after analyzing : 20, 32, 36, 39 LEFT_CER before analyzing : 20, 22, 28, 62 after analyzing : 20, 26, 28, 35 RIGHT_BRAIN before analyzing : 35, 34, 34, 56 after analyzing : 26, 34, 34, 39 LEFT_BRAIN before analyzing : 36, 34, 33, 56 after analyzing : 26, 34, 34, 39 OTHER before analyzing : 36, 65, 81, 94 after analyzing : 36, 75, 81, 79 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...74 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 67.605, std = 7.157 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.51, sigma = 6.02 after rotation: sse = 4.51, sigma = 6.02 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.06, its var is 6.98 before Erosion-Dilatation 1.99% of inacurate vertices after Erosion-Dilatation 1.92% 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...35 iterations mri_strip_skull: done peeling brain Brain Size = 1496715 voxels, voxel volume = 1.000 mm3 = 1496715 mmm3 = 1496.715 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 24.273309 mri_watershed stimesec 0.423935 mri_watershed ru_maxrss 825752 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 213776 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2440 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1625 mri_watershed ru_nivcsw 93 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 18:01:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 2 == 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=25.0 skull bounding box = (58, 52, 44) --> (192, 188, 191) using (103, 97, 118) as brain centroid... mean wm in atlas = 107, using box (87,80,100) --> (119, 113,136) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.8 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.171 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.992748 @ (9.091, 9.091, -9.091) max log p = -3.828710 @ (-4.545, -4.545, -4.545) max log p = -3.828710 @ (0.000, 0.000, 0.000) max log p = -3.797133 @ (1.136, 3.409, 1.136) max log p = -3.788119 @ (-0.568, -0.568, 0.568) max log p = -3.785866 @ (-0.284, 0.284, 0.852) Found translation: (4.8, 7.7, -11.1): log p = -3.786 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.429, old_max_log_p =-3.786 (thresh=-3.8) 1.07500 0.00000 0.00000 -4.31354; 0.00000 1.06753 0.42117 -48.94395; 0.00000 -0.43171 0.98772 46.03884; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.429, old_max_log_p =-3.429 (thresh=-3.4) 1.07500 0.00000 0.00000 -4.31354; 0.00000 1.06753 0.42117 -48.94395; 0.00000 -0.43171 0.98772 46.03884; 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=-3.227, old_max_log_p =-3.429 (thresh=-3.4) 1.03415 -0.04082 -0.01630 5.25701; 0.03773 1.11140 0.36428 -50.53644; -0.00253 -0.36516 1.03299 31.64216; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.211, old_max_log_p =-3.227 (thresh=-3.2) 1.03415 -0.01795 0.03010 -2.47598; 0.00373 1.07941 0.38966 -45.57224; -0.03759 -0.39978 1.02050 41.24948; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.211, old_max_log_p =-3.211 (thresh=-3.2) 1.03415 -0.01795 0.03010 -2.47598; 0.00373 1.07941 0.38966 -45.57224; -0.03759 -0.39978 1.02050 41.24948; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.174, old_max_log_p =-3.211 (thresh=-3.2) 1.03273 -0.03557 0.02370 0.38734; 0.02036 1.07693 0.39888 -48.83958; -0.03772 -0.40814 1.01608 43.63070; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.173, old_max_log_p =-3.174 (thresh=-3.2) 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 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 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.173 (old=-4.171) transform before final EM align: 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 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 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.7 tol 0.000000 final transform: 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1104.946022 mri_em_register stimesec 1.396787 mri_em_register ru_maxrss 599052 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158953 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 94 mri_em_register ru_nivcsw 3317 registration took 9 minutes and 31 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 18:11:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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=25.0 skull bounding box = (58, 52, 44) --> (192, 188, 191) using (103, 97, 118) as brain centroid... mean wm in atlas = 107, using box (87,80,100) --> (119, 113,136) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.8 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.03374 -0.04445 0.02053 1.61643; 0.02912 1.07990 0.39074 -49.35633; -0.03759 -0.39978 1.02050 41.71447; 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 (123, 55, 44) --> (188, 161, 193) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 375 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 55, 43) --> (124, 155, 192) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 304 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 137, 75) --> (174, 174, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 7 (100.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 138, 71) --> (125, 174, 124) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 122, 104) --> (142, 183, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 27 (0.0%) samples deleted using 722 total control points for intensity normalization... bias field = 0.954 +- 0.052 7 of 715 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 55, 44) --> (188, 161, 193) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 494 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 55, 43) --> (124, 155, 192) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 465 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 137, 75) --> (174, 174, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 53 (11.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 138, 71) --> (125, 174, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 48 (12.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 122, 104) --> (142, 183, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 53 of 98 (54.1%) samples deleted using 1158 total control points for intensity normalization... bias field = 1.009 +- 0.056 4 of 1071 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 55, 44) --> (188, 161, 193) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 584 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 55, 43) --> (124, 155, 192) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 551 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 137, 75) --> (174, 174, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 79 (16.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 138, 71) --> (125, 174, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 44 of 89 (49.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 122, 104) --> (142, 183, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 152 of 188 (80.9%) samples deleted using 1491 total control points for intensity normalization... bias field = 1.008 +- 0.048 4 of 1242 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 18:13:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 2 == 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) = 1.30 (predicted orig area = 6.1) 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=0.770, neg=0, invalid=762 0001: dt=208.753927, rms=0.725 (5.918%), neg=0, invalid=762 0002: dt=218.378378, rms=0.711 (1.883%), neg=0, invalid=762 0003: dt=162.796117, rms=0.705 (0.851%), neg=0, invalid=762 0004: dt=443.904000, rms=0.697 (1.214%), neg=0, invalid=762 0005: dt=110.976000, rms=0.693 (0.588%), neg=0, invalid=762 0006: dt=1479.680000, rms=0.681 (1.677%), neg=0, invalid=762 0007: dt=129.472000, rms=0.679 (0.322%), neg=0, invalid=762 0008: dt=295.936000, rms=0.677 (0.185%), neg=0, invalid=762 0009: dt=295.936000, rms=0.677 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0010: dt=129.472000, rms=0.676 (0.276%), neg=0, invalid=762 0011: dt=1183.744000, rms=0.673 (0.542%), neg=0, invalid=762 0012: dt=221.952000, rms=0.670 (0.315%), neg=0, invalid=762 0013: dt=129.472000, rms=0.670 (0.044%), neg=0, invalid=762 0014: dt=129.472000, rms=0.670 (0.044%), neg=0, invalid=762 0015: dt=129.472000, rms=0.669 (0.076%), neg=0, invalid=762 0016: dt=129.472000, rms=0.669 (0.105%), neg=0, invalid=762 0017: dt=129.472000, rms=0.668 (0.127%), neg=0, invalid=762 0018: dt=129.472000, rms=0.667 (0.152%), neg=0, invalid=762 0019: dt=129.472000, rms=0.666 (0.169%), neg=0, invalid=762 0020: dt=129.472000, rms=0.664 (0.176%), neg=0, invalid=762 0021: dt=129.472000, rms=0.663 (0.159%), neg=0, invalid=762 0022: dt=129.472000, rms=0.662 (0.149%), neg=0, invalid=762 0023: dt=129.472000, rms=0.661 (0.149%), neg=0, invalid=762 0024: dt=129.472000, rms=0.660 (0.148%), neg=0, invalid=762 0025: dt=129.472000, rms=0.660 (0.141%), neg=0, invalid=762 0026: dt=129.472000, rms=0.659 (0.137%), neg=0, invalid=762 0027: dt=129.472000, rms=0.658 (0.128%), neg=0, invalid=762 0028: dt=129.472000, rms=0.657 (0.118%), neg=0, invalid=762 0029: dt=129.472000, rms=0.656 (0.112%), neg=0, invalid=762 0030: dt=1479.680000, rms=0.656 (0.095%), neg=0, invalid=762 0031: dt=1479.680000, rms=0.656 (-5.418%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.659, neg=0, invalid=762 0032: dt=145.152000, rms=0.652 (1.181%), neg=0, invalid=762 0033: dt=121.379310, rms=0.646 (0.875%), neg=0, invalid=762 0034: dt=79.029024, rms=0.641 (0.724%), neg=0, invalid=762 0035: dt=111.304348, rms=0.638 (0.449%), neg=0, invalid=762 0036: dt=89.132420, rms=0.635 (0.541%), neg=0, invalid=762 0037: dt=78.940767, rms=0.633 (0.308%), neg=0, invalid=762 0038: dt=141.241379, rms=0.630 (0.461%), neg=0, invalid=762 0039: dt=36.288000, rms=0.628 (0.252%), neg=0, invalid=762 0040: dt=145.152000, rms=0.626 (0.334%), neg=0, invalid=762 0041: dt=94.986425, rms=0.624 (0.317%), neg=0, invalid=762 0042: dt=64.876712, rms=0.623 (0.160%), neg=0, invalid=762 0043: dt=64.876712, rms=0.622 (0.202%), neg=0, invalid=762 0044: dt=64.876712, rms=0.620 (0.271%), neg=0, invalid=762 0045: dt=64.876712, rms=0.618 (0.360%), neg=0, invalid=762 0046: dt=64.876712, rms=0.616 (0.400%), neg=0, invalid=762 0047: dt=64.876712, rms=0.613 (0.477%), neg=0, invalid=762 0048: dt=64.876712, rms=0.610 (0.472%), neg=0, invalid=762 0049: dt=64.876712, rms=0.607 (0.429%), neg=0, invalid=762 0050: dt=64.876712, rms=0.605 (0.390%), neg=0, invalid=762 0051: dt=64.876712, rms=0.603 (0.356%), neg=0, invalid=762 0052: dt=64.876712, rms=0.601 (0.320%), neg=0, invalid=762 0053: dt=64.876712, rms=0.599 (0.257%), neg=0, invalid=762 0054: dt=64.876712, rms=0.598 (0.209%), neg=0, invalid=762 0055: dt=64.876712, rms=0.597 (0.170%), neg=0, invalid=762 0056: dt=64.876712, rms=0.596 (0.172%), neg=0, invalid=762 0057: dt=64.876712, rms=0.595 (0.135%), neg=0, invalid=762 0058: dt=64.876712, rms=0.595 (0.106%), neg=0, invalid=762 0059: dt=64.876712, rms=0.594 (0.088%), neg=0, invalid=762 0060: dt=145.152000, rms=0.594 (0.044%), neg=0, invalid=762 0061: dt=145.152000, rms=0.594 (-0.103%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.594, neg=0, invalid=762 0062: dt=67.537688, rms=0.593 (0.258%), neg=0, invalid=762 0063: dt=145.152000, rms=0.592 (0.200%), neg=0, invalid=762 0064: dt=145.152000, rms=0.592 (-0.533%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0065: dt=2.800000, rms=0.612 (0.118%), neg=0, invalid=762 0066: dt=1.600000, rms=0.612 (0.005%), neg=0, invalid=762 0067: dt=1.600000, rms=0.612 (0.001%), neg=0, invalid=762 0068: dt=1.600000, rms=0.612 (-0.021%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=762 0069: dt=0.700000, rms=0.612 (0.093%), neg=0, invalid=762 0070: dt=0.125000, rms=0.612 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0071: dt=5.568493, rms=0.652 (2.665%), neg=0, invalid=762 0072: dt=2.160000, rms=0.652 (0.081%), neg=0, invalid=762 0073: dt=2.160000, rms=0.652 (-0.027%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0074: dt=0.000000, rms=0.652 (0.076%), neg=0, invalid=762 0075: dt=0.000000, rms=0.652 (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=0.705, neg=0, invalid=762 0076: dt=1.280000, rms=0.701 (0.575%), neg=0, invalid=762 0077: dt=2.043478, rms=0.696 (0.763%), neg=0, invalid=762 0078: dt=0.320000, rms=0.696 (0.017%), neg=0, invalid=762 0079: dt=0.320000, rms=0.696 (0.016%), neg=0, invalid=762 0080: dt=0.320000, rms=0.696 (0.015%), neg=0, invalid=762 0081: dt=0.320000, rms=0.696 (0.001%), neg=0, invalid=762 0082: dt=1.792000, rms=0.695 (0.165%), neg=0, invalid=762 0083: dt=0.000000, rms=0.695 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0084: dt=0.768000, rms=0.694 (0.143%), neg=0, invalid=762 0085: dt=1.536000, rms=0.694 (0.041%), neg=0, invalid=762 0086: dt=1.536000, rms=0.694 (-0.040%), 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=0.666, neg=0, invalid=762 0087: dt=0.855208, rms=0.647 (2.819%), neg=0, invalid=762 0088: dt=0.080000, rms=0.646 (0.147%), neg=0, invalid=762 0089: dt=0.080000, rms=0.646 (-0.089%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.647, neg=0, invalid=762 0090: dt=0.028000, rms=0.646 (0.097%), neg=0, invalid=762 0091: dt=0.007000, rms=0.646 (0.001%), neg=0, invalid=762 0092: dt=0.007000, rms=0.646 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.13839 (10) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (517 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (517 voxels, peak = 8), gca=8.1 gca peak = 0.15565 (16) mri peak = 0.07958 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (423 voxels, overlap=0.119) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (423 voxels, peak = 8), gca=8.2 gca peak = 0.26829 (96) mri peak = 0.07753 (84) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (683 voxels, overlap=0.109) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (683 voxels, peak = 87), gca=86.9 gca peak = 0.20183 (93) mri peak = 0.06283 (83) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (513 voxels, overlap=0.599) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (513 voxels, peak = 85), gca=85.1 gca peak = 0.21683 (55) mri peak = 0.09181 (54) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (556 voxels, overlap=0.989) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (556 voxels, peak = 53), gca=53.1 gca peak = 0.30730 (58) mri peak = 0.09663 (55) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (591 voxels, overlap=0.963) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (591 voxels, peak = 54), gca=54.2 gca peak = 0.11430 (101) mri peak = 0.09126 (104) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (54149 voxels, overlap=0.748) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (54149 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.09353 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54013 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54013 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04425 (58) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (18643 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (18643 voxels, peak = 56), gca=55.8 gca peak = 0.15082 (58) mri peak = 0.04959 (51) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (18062 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (18062 voxels, peak = 53), gca=53.1 gca peak = 0.14161 (67) mri peak = 0.08290 (67) Right_Caudate (50): linear fit = 0.99 x + 0.0 (875 voxels, overlap=0.988) Right_Caudate (50): linear fit = 0.99 x + 0.0 (875 voxels, peak = 66), gca=66.0 gca peak = 0.15243 (71) mri peak = 0.08190 (69) Left_Caudate (11): linear fit = 0.94 x + 0.0 (762 voxels, overlap=0.858) Left_Caudate (11): linear fit = 0.94 x + 0.0 (762 voxels, peak = 66), gca=66.4 gca peak = 0.13336 (57) mri peak = 0.04368 (55) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (16574 voxels, overlap=0.976) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (16574 voxels, peak = 57), gca=57.0 gca peak = 0.13252 (56) mri peak = 0.04346 (51) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (20106 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (20106 voxels, peak = 53), gca=52.9 gca peak = 0.18181 (84) mri peak = 0.06300 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6214 voxels, overlap=0.634) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6214 voxels, peak = 92), gca=92.0 gca peak = 0.20573 (83) mri peak = 0.07176 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5738 voxels, overlap=0.924) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5738 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.09351 (57) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (378 voxels, overlap=0.977) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (378 voxels, peak = 54), gca=53.9 gca peak = 0.39313 (56) mri peak = 0.10663 (54) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (448 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (448 voxels, peak = 53), gca=52.9 gca peak = 0.14181 (85) mri peak = 0.05894 (84) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4976 voxels, overlap=0.969) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4976 voxels, peak = 83), gca=82.9 gca peak = 0.11978 (83) mri peak = 0.07145 (83) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4273 voxels, overlap=0.928) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4273 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.07639 (73) Left_Putamen (12): linear fit = 0.96 x + 0.0 (2030 voxels, overlap=0.845) Left_Putamen (12): linear fit = 0.96 x + 0.0 (2030 voxels, peak = 76), gca=76.2 gca peak = 0.14159 (79) mri peak = 0.07807 (72) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2035 voxels, overlap=0.886) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2035 voxels, peak = 76), gca=76.2 gca peak = 0.10025 (80) mri peak = 0.12785 (80) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9743 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9743 voxels, peak = 85), gca=85.2 gca peak = 0.13281 (86) mri peak = 0.09188 (86) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (804 voxels, overlap=0.719) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (804 voxels, peak = 87), gca=87.3 gca peak = 0.12801 (89) mri peak = 0.08987 (87) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (823 voxels, overlap=0.834) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (823 voxels, peak = 89), gca=88.6 gca peak = 0.20494 (23) mri peak = 0.10264 (38) gca peak = 0.15061 (21) mri peak = 0.13416 (10) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (206 voxels, overlap=0.285) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (206 voxels, peak = 9), gca=9.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) 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 estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.46 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=0.674, neg=0, invalid=762 0093: dt=147.744681, rms=0.669 (0.751%), neg=0, invalid=762 0094: dt=295.936000, rms=0.665 (0.585%), neg=0, invalid=762 0095: dt=92.480000, rms=0.663 (0.216%), neg=0, invalid=762 0096: dt=443.904000, rms=0.661 (0.378%), neg=0, invalid=762 0097: dt=73.984000, rms=0.660 (0.146%), neg=0, invalid=762 0098: dt=1183.744000, rms=0.658 (0.362%), neg=0, invalid=762 0099: dt=110.976000, rms=0.657 (0.149%), neg=0, invalid=762 0100: dt=110.976000, rms=0.656 (0.032%), neg=0, invalid=762 0101: dt=110.976000, rms=0.656 (0.039%), neg=0, invalid=762 0102: dt=110.976000, rms=0.656 (0.055%), neg=0, invalid=762 0103: dt=110.976000, rms=0.655 (0.067%), neg=0, invalid=762 0104: dt=110.976000, rms=0.655 (0.074%), neg=0, invalid=762 0105: dt=110.976000, rms=0.654 (0.089%), neg=0, invalid=762 0106: dt=110.976000, rms=0.654 (0.088%), neg=0, invalid=762 0107: dt=110.976000, rms=0.653 (0.081%), neg=0, invalid=762 0108: dt=110.976000, rms=0.653 (0.077%), neg=0, invalid=762 0109: dt=110.976000, rms=0.652 (0.083%), neg=0, invalid=762 0110: dt=110.976000, rms=0.652 (0.083%), neg=0, invalid=762 0111: dt=110.976000, rms=0.651 (0.077%), neg=0, invalid=762 0112: dt=110.976000, rms=0.651 (0.068%), neg=0, invalid=762 0113: dt=110.976000, rms=0.650 (0.065%), neg=0, invalid=762 0114: dt=110.976000, rms=0.650 (0.065%), neg=0, invalid=762 0115: dt=110.976000, rms=0.649 (0.065%), neg=0, invalid=762 0116: dt=110.976000, rms=0.649 (0.065%), neg=0, invalid=762 0117: dt=110.976000, rms=0.648 (0.064%), neg=0, invalid=762 0118: dt=110.976000, rms=0.648 (0.063%), neg=0, invalid=762 0119: dt=110.976000, rms=0.648 (0.064%), neg=0, invalid=762 0120: dt=110.976000, rms=0.647 (0.061%), neg=0, invalid=762 0121: dt=110.976000, rms=0.647 (0.055%), neg=0, invalid=762 0122: dt=110.976000, rms=0.647 (0.054%), neg=0, invalid=762 0123: dt=110.976000, rms=0.646 (0.054%), neg=0, invalid=762 0124: dt=110.976000, rms=0.646 (0.055%), neg=0, invalid=762 0125: dt=110.976000, rms=0.646 (0.052%), neg=0, invalid=762 0126: dt=110.976000, rms=0.645 (0.049%), neg=0, invalid=762 0127: dt=110.976000, rms=0.645 (0.047%), neg=0, invalid=762 0128: dt=110.976000, rms=0.645 (0.046%), neg=0, invalid=762 0129: dt=110.976000, rms=0.644 (0.042%), neg=0, invalid=762 0130: dt=110.976000, rms=0.644 (0.041%), neg=0, invalid=762 0131: dt=110.976000, rms=0.644 (0.041%), neg=0, invalid=762 0132: dt=110.976000, rms=0.644 (0.039%), neg=0, invalid=762 0133: dt=110.976000, rms=0.643 (0.039%), neg=0, invalid=762 0134: dt=110.976000, rms=0.643 (0.033%), neg=0, invalid=762 0135: dt=110.976000, rms=0.643 (0.033%), neg=0, invalid=762 0136: dt=110.976000, rms=0.643 (0.036%), neg=0, invalid=762 0137: dt=110.976000, rms=0.642 (0.034%), neg=0, invalid=762 0138: dt=110.976000, rms=0.642 (0.030%), neg=0, invalid=762 0139: dt=110.976000, rms=0.642 (0.030%), neg=0, invalid=762 0140: dt=110.976000, rms=0.642 (0.032%), neg=0, invalid=762 0141: dt=110.976000, rms=0.642 (0.032%), neg=0, invalid=762 0142: dt=110.976000, rms=0.641 (0.029%), neg=0, invalid=762 0143: dt=110.976000, rms=0.641 (0.025%), neg=0, invalid=762 0144: dt=110.976000, rms=0.641 (0.024%), neg=0, invalid=762 0145: dt=2071.552000, rms=0.641 (0.053%), neg=0, invalid=762 0146: dt=32.368000, rms=0.641 (0.008%), neg=0, invalid=762 0147: dt=32.368000, rms=0.641 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.641, neg=0, invalid=762 0148: dt=110.976000, rms=0.640 (0.159%), neg=0, invalid=762 0149: dt=517.888000, rms=0.640 (0.130%), neg=0, invalid=762 0150: dt=32.368000, rms=0.640 (0.008%), neg=0, invalid=762 0151: dt=32.368000, rms=0.639 (0.002%), neg=0, invalid=762 0152: dt=32.368000, rms=0.640 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.641, neg=0, invalid=762 0153: dt=103.239344, rms=0.637 (0.630%), neg=0, invalid=762 0154: dt=98.114537, rms=0.633 (0.664%), neg=0, invalid=762 0155: dt=61.333333, rms=0.630 (0.405%), neg=0, invalid=762 0156: dt=103.680000, rms=0.627 (0.447%), neg=0, invalid=762 0157: dt=36.288000, rms=0.625 (0.315%), neg=0, invalid=762 0158: dt=580.608000, rms=0.617 (1.354%), neg=0, invalid=762 0159: dt=69.500000, rms=0.613 (0.603%), neg=0, invalid=762 0160: dt=36.288000, rms=0.612 (0.151%), neg=0, invalid=762 0161: dt=497.664000, rms=0.610 (0.392%), neg=0, invalid=762 0162: dt=62.923077, rms=0.606 (0.575%), neg=0, invalid=762 0163: dt=36.288000, rms=0.606 (0.061%), neg=0, invalid=762 0164: dt=580.608000, rms=0.603 (0.400%), neg=0, invalid=762 0165: dt=64.458781, rms=0.601 (0.388%), neg=0, invalid=762 0166: dt=36.288000, rms=0.601 (0.040%), neg=0, invalid=762 0167: dt=36.288000, rms=0.601 (0.030%), neg=0, invalid=762 0168: dt=36.288000, rms=0.600 (0.057%), neg=0, invalid=762 0169: dt=36.288000, rms=0.600 (0.085%), neg=0, invalid=762 0170: dt=36.288000, rms=0.599 (0.112%), neg=0, invalid=762 0171: dt=36.288000, rms=0.598 (0.132%), neg=0, invalid=762 0172: dt=36.288000, rms=0.598 (0.149%), neg=0, invalid=762 0173: dt=36.288000, rms=0.597 (0.145%), neg=0, invalid=762 0174: dt=36.288000, rms=0.596 (0.151%), neg=0, invalid=762 0175: dt=36.288000, rms=0.595 (0.148%), neg=0, invalid=762 0176: dt=36.288000, rms=0.594 (0.156%), neg=0, invalid=762 0177: dt=36.288000, rms=0.593 (0.152%), neg=0, invalid=762 0178: dt=36.288000, rms=0.592 (0.146%), neg=0, invalid=762 0179: dt=36.288000, rms=0.591 (0.135%), neg=0, invalid=762 0180: dt=36.288000, rms=0.591 (0.014%), neg=0, invalid=762 0181: dt=36.288000, rms=0.591 (0.025%), neg=0, invalid=762 0182: dt=36.288000, rms=0.591 (0.042%), neg=0, invalid=762 0183: dt=36.288000, rms=0.591 (0.050%), neg=0, invalid=762 0184: dt=36.288000, rms=0.590 (0.062%), neg=0, invalid=762 0185: dt=36.288000, rms=0.590 (0.066%), neg=0, invalid=762 0186: dt=36.288000, rms=0.589 (0.071%), neg=0, invalid=762 0187: dt=36.288000, rms=0.589 (0.074%), neg=0, invalid=762 0188: dt=36.288000, rms=0.589 (0.017%), neg=0, invalid=762 0189: dt=18.144000, rms=0.589 (0.006%), neg=0, invalid=762 0190: dt=9.072000, rms=0.589 (0.004%), neg=0, invalid=762 0191: dt=2.268000, rms=0.589 (0.001%), neg=0, invalid=762 0192: dt=0.070875, rms=0.589 (0.000%), neg=0, invalid=762 0193: dt=0.004430, rms=0.589 (0.001%), neg=0, invalid=762 0194: dt=0.002215, rms=0.589 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=762 0195: dt=84.317460, rms=0.587 (0.407%), neg=0, invalid=762 0196: dt=82.944000, rms=0.586 (0.201%), neg=0, invalid=762 0197: dt=36.288000, rms=0.585 (0.082%), neg=0, invalid=762 0198: dt=580.608000, rms=0.583 (0.423%), neg=0, invalid=762 0199: dt=36.288000, rms=0.582 (0.114%), neg=0, invalid=762 0200: dt=145.152000, rms=0.582 (0.091%), neg=0, invalid=762 0201: dt=36.288000, rms=0.582 (0.010%), neg=0, invalid=762 0202: dt=36.288000, rms=0.582 (0.018%), neg=0, invalid=762 0203: dt=36.288000, rms=0.581 (0.033%), neg=0, invalid=762 0204: dt=36.288000, rms=0.581 (0.041%), neg=0, invalid=762 0205: dt=36.288000, rms=0.581 (0.054%), neg=0, invalid=762 0206: dt=36.288000, rms=0.581 (0.060%), neg=0, invalid=762 0207: dt=36.288000, rms=0.580 (0.066%), neg=0, invalid=762 0208: dt=36.288000, rms=0.580 (0.070%), neg=0, invalid=762 0209: dt=36.288000, rms=0.579 (0.075%), neg=0, invalid=762 0210: dt=36.288000, rms=0.579 (0.080%), neg=0, invalid=762 0211: dt=36.288000, rms=0.578 (0.086%), neg=0, invalid=762 0212: dt=36.288000, rms=0.578 (0.084%), neg=0, invalid=762 0213: dt=36.288000, rms=0.577 (0.087%), neg=0, invalid=762 0214: dt=36.288000, rms=0.577 (0.087%), neg=0, invalid=762 0215: dt=36.288000, rms=0.576 (0.084%), neg=0, invalid=762 0216: dt=36.288000, rms=0.576 (0.083%), neg=0, invalid=762 0217: dt=36.288000, rms=0.575 (0.080%), neg=0, invalid=762 0218: dt=36.288000, rms=0.575 (0.079%), neg=0, invalid=762 0219: dt=36.288000, rms=0.575 (0.075%), neg=0, invalid=762 0220: dt=36.288000, rms=0.574 (0.075%), neg=0, invalid=762 0221: dt=36.288000, rms=0.574 (0.076%), neg=0, invalid=762 0222: dt=36.288000, rms=0.573 (0.073%), neg=0, invalid=762 0223: dt=36.288000, rms=0.573 (0.069%), neg=0, invalid=762 0224: dt=36.288000, rms=0.572 (0.070%), neg=0, invalid=762 0225: dt=36.288000, rms=0.572 (0.067%), neg=0, invalid=762 0226: dt=36.288000, rms=0.572 (0.071%), neg=0, invalid=762 0227: dt=36.288000, rms=0.571 (0.068%), neg=0, invalid=762 0228: dt=36.288000, rms=0.571 (0.065%), neg=0, invalid=762 0229: dt=36.288000, rms=0.571 (0.065%), neg=0, invalid=762 0230: dt=36.288000, rms=0.570 (0.062%), neg=0, invalid=762 0231: dt=36.288000, rms=0.570 (0.060%), neg=0, invalid=762 0232: dt=36.288000, rms=0.570 (0.060%), neg=0, invalid=762 0233: dt=36.288000, rms=0.569 (0.059%), neg=0, invalid=762 0234: dt=36.288000, rms=0.569 (0.056%), neg=0, invalid=762 0235: dt=36.288000, rms=0.569 (0.056%), neg=0, invalid=762 0236: dt=36.288000, rms=0.568 (0.056%), neg=0, invalid=762 0237: dt=36.288000, rms=0.568 (0.054%), neg=0, invalid=762 0238: dt=36.288000, rms=0.568 (0.057%), neg=0, invalid=762 0239: dt=36.288000, rms=0.567 (0.054%), neg=0, invalid=762 0240: dt=36.288000, rms=0.567 (0.051%), neg=0, invalid=762 0241: dt=36.288000, rms=0.567 (0.051%), neg=0, invalid=762 0242: dt=36.288000, rms=0.566 (0.049%), neg=0, invalid=762 0243: dt=36.288000, rms=0.566 (0.048%), neg=0, invalid=762 0244: dt=36.288000, rms=0.566 (0.046%), neg=0, invalid=762 0245: dt=36.288000, rms=0.566 (0.046%), neg=0, invalid=762 0246: dt=36.288000, rms=0.565 (0.047%), neg=0, invalid=762 0247: dt=36.288000, rms=0.565 (0.044%), neg=0, invalid=762 0248: dt=36.288000, rms=0.565 (0.044%), neg=0, invalid=762 0249: dt=36.288000, rms=0.565 (0.040%), neg=0, invalid=762 0250: dt=36.288000, rms=0.564 (0.040%), neg=0, invalid=762 0251: dt=36.288000, rms=0.564 (0.037%), neg=0, invalid=762 0252: dt=36.288000, rms=0.564 (0.038%), neg=0, invalid=762 0253: dt=36.288000, rms=0.564 (0.036%), neg=0, invalid=762 0254: dt=36.288000, rms=0.564 (0.037%), neg=0, invalid=762 0255: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762 0256: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762 0257: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762 0258: dt=36.288000, rms=0.563 (0.036%), neg=0, invalid=762 0259: dt=36.288000, rms=0.563 (0.038%), neg=0, invalid=762 0260: dt=36.288000, rms=0.562 (0.035%), neg=0, invalid=762 0261: dt=36.288000, rms=0.562 (0.031%), neg=0, invalid=762 0262: dt=36.288000, rms=0.562 (0.032%), neg=0, invalid=762 0263: dt=36.288000, rms=0.562 (0.027%), neg=0, invalid=762 0264: dt=36.288000, rms=0.562 (0.032%), neg=0, invalid=762 0265: dt=36.288000, rms=0.562 (0.031%), neg=0, invalid=762 0266: dt=36.288000, rms=0.561 (0.028%), neg=0, invalid=762 0267: dt=36.288000, rms=0.561 (0.027%), neg=0, invalid=762 0268: dt=36.288000, rms=0.561 (0.028%), neg=0, invalid=762 0269: dt=36.288000, rms=0.561 (0.029%), neg=0, invalid=762 0270: dt=36.288000, rms=0.561 (0.026%), neg=0, invalid=762 0271: dt=36.288000, rms=0.561 (0.023%), neg=0, invalid=762 0272: dt=36.288000, rms=0.561 (0.026%), neg=0, invalid=762 0273: dt=36.288000, rms=0.560 (0.024%), neg=0, invalid=762 0274: dt=36.288000, rms=0.560 (0.028%), neg=0, invalid=762 0275: dt=36.288000, rms=0.560 (0.026%), neg=0, invalid=762 0276: dt=36.288000, rms=0.560 (0.022%), neg=0, invalid=762 0277: dt=36.288000, rms=0.560 (0.023%), neg=0, invalid=762 0278: dt=36.288000, rms=0.560 (0.023%), neg=0, invalid=762 0279: dt=36.288000, rms=0.560 (0.023%), neg=0, invalid=762 0280: dt=145.152000, rms=0.560 (0.003%), neg=0, invalid=762 0281: dt=145.152000, rms=0.559 (0.013%), neg=0, invalid=762 0282: dt=145.152000, rms=0.559 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.567, neg=0, invalid=762 0283: dt=22.787879, rms=0.565 (0.377%), neg=0, invalid=762 0284: dt=77.195876, rms=0.561 (0.622%), neg=0, invalid=762 0285: dt=11.200000, rms=0.559 (0.313%), neg=0, invalid=762 0286: dt=11.200000, rms=0.558 (0.182%), neg=0, invalid=762 0287: dt=11.200000, rms=0.557 (0.164%), neg=0, invalid=762 0288: dt=2.800000, rms=0.557 (0.040%), neg=0, invalid=762 0289: dt=1.400000, rms=0.557 (0.020%), neg=0, invalid=762 0290: dt=0.700000, rms=0.557 (0.009%), neg=0, invalid=762 0291: dt=0.350000, rms=0.557 (0.005%), neg=0, invalid=762 0292: dt=0.175000, rms=0.557 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 0293: dt=38.004751, rms=0.553 (0.862%), neg=0, invalid=762 0294: dt=24.016360, rms=0.550 (0.459%), neg=0, invalid=762 0295: dt=25.600000, rms=0.549 (0.260%), neg=0, invalid=762 0296: dt=31.695238, rms=0.547 (0.280%), neg=0, invalid=762 0297: dt=11.200000, rms=0.546 (0.191%), neg=0, invalid=762 0298: dt=153.600000, rms=0.543 (0.673%), neg=0, invalid=762 0299: dt=18.541176, rms=0.540 (0.531%), neg=0, invalid=762 0300: dt=25.600000, rms=0.539 (0.127%), neg=0, invalid=762 0301: dt=25.600000, rms=0.538 (0.140%), neg=0, invalid=762 0302: dt=19.200000, rms=0.538 (0.117%), neg=0, invalid=762 0303: dt=38.400000, rms=0.537 (0.141%), neg=0, invalid=762 0304: dt=11.200000, rms=0.536 (0.106%), neg=0, invalid=762 0305: dt=179.200000, rms=0.533 (0.561%), neg=0, invalid=762 0306: dt=11.200000, rms=0.532 (0.221%), neg=0, invalid=762 0307: dt=38.400000, rms=0.532 (0.082%), neg=0, invalid=762 0308: dt=11.200000, rms=0.532 (0.064%), neg=0, invalid=762 0309: dt=179.200000, rms=0.530 (0.310%), neg=0, invalid=762 0310: dt=11.200000, rms=0.529 (0.183%), neg=0, invalid=762 0311: dt=25.600000, rms=0.528 (0.091%), neg=0, invalid=762 0312: dt=32.000000, rms=0.528 (0.081%), neg=0, invalid=762 0313: dt=11.200000, rms=0.528 (0.037%), neg=0, invalid=762 0314: dt=11.200000, rms=0.528 (0.027%), neg=0, invalid=762 0315: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=762 0316: dt=11.200000, rms=0.527 (0.066%), neg=0, invalid=762 0317: dt=11.200000, rms=0.527 (0.078%), neg=0, invalid=762 0318: dt=11.200000, rms=0.526 (0.097%), neg=0, invalid=762 0319: dt=11.200000, rms=0.526 (0.103%), neg=0, invalid=762 0320: dt=11.200000, rms=0.525 (0.108%), neg=0, invalid=762 0321: dt=11.200000, rms=0.524 (0.120%), neg=0, invalid=762 0322: dt=11.200000, rms=0.524 (0.125%), neg=0, invalid=762 0323: dt=11.200000, rms=0.523 (0.125%), neg=0, invalid=762 0324: dt=11.200000, rms=0.522 (0.132%), neg=0, invalid=762 0325: dt=11.200000, rms=0.522 (0.128%), neg=0, invalid=762 0326: dt=11.200000, rms=0.521 (0.129%), neg=0, invalid=762 0327: dt=11.200000, rms=0.520 (0.129%), neg=0, invalid=762 0328: dt=11.200000, rms=0.520 (0.122%), neg=0, invalid=762 0329: dt=11.200000, rms=0.519 (0.121%), neg=0, invalid=762 0330: dt=11.200000, rms=0.519 (0.116%), neg=0, invalid=762 0331: dt=11.200000, rms=0.518 (0.107%), neg=0, invalid=762 0332: dt=11.200000, rms=0.517 (0.108%), neg=0, invalid=762 0333: dt=11.200000, rms=0.517 (0.099%), neg=0, invalid=762 0334: dt=11.200000, rms=0.516 (0.093%), neg=0, invalid=762 0335: dt=11.200000, rms=0.516 (0.089%), neg=0, invalid=762 0336: dt=11.200000, rms=0.516 (0.086%), neg=0, invalid=762 0337: dt=11.200000, rms=0.515 (0.084%), neg=0, invalid=762 0338: dt=11.200000, rms=0.515 (0.072%), neg=0, invalid=762 0339: dt=11.200000, rms=0.514 (0.072%), neg=0, invalid=762 0340: dt=11.200000, rms=0.514 (0.068%), neg=0, invalid=762 0341: dt=11.200000, rms=0.514 (0.066%), neg=0, invalid=762 0342: dt=11.200000, rms=0.513 (0.059%), neg=0, invalid=762 0343: dt=11.200000, rms=0.513 (0.055%), neg=0, invalid=762 0344: dt=11.200000, rms=0.513 (0.055%), neg=0, invalid=762 0345: dt=11.200000, rms=0.513 (0.050%), neg=0, invalid=762 0346: dt=11.200000, rms=0.512 (0.045%), neg=0, invalid=762 0347: dt=11.200000, rms=0.512 (0.042%), neg=0, invalid=762 0348: dt=11.200000, rms=0.512 (0.048%), neg=0, invalid=762 0349: dt=11.200000, rms=0.512 (0.041%), neg=0, invalid=762 0350: dt=11.200000, rms=0.511 (0.036%), neg=0, invalid=762 0351: dt=11.200000, rms=0.511 (0.038%), neg=0, invalid=762 0352: dt=11.200000, rms=0.511 (0.038%), neg=0, invalid=762 0353: dt=11.200000, rms=0.511 (0.037%), neg=0, invalid=762 0354: dt=11.200000, rms=0.511 (0.035%), neg=0, invalid=762 0355: dt=11.200000, rms=0.511 (0.032%), neg=0, invalid=762 0356: dt=11.200000, rms=0.510 (0.034%), neg=0, invalid=762 0357: dt=11.200000, rms=0.510 (0.036%), neg=0, invalid=762 0358: dt=11.200000, rms=0.510 (0.033%), neg=0, invalid=762 0359: dt=11.200000, rms=0.510 (0.031%), neg=0, invalid=762 0360: dt=11.200000, rms=0.510 (0.035%), neg=0, invalid=762 0361: dt=11.200000, rms=0.510 (0.028%), neg=0, invalid=762 0362: dt=11.200000, rms=0.509 (0.029%), neg=0, invalid=762 0363: dt=11.200000, rms=0.509 (0.032%), neg=0, invalid=762 0364: dt=11.200000, rms=0.509 (0.024%), neg=0, invalid=762 0365: dt=11.200000, rms=0.509 (0.024%), neg=0, invalid=762 0366: dt=32.000000, rms=0.509 (0.007%), neg=0, invalid=762 0367: dt=32.000000, rms=0.509 (-0.014%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.528, neg=0, invalid=762 0368: dt=0.000000, rms=0.527 (0.145%), neg=0, invalid=762 0369: dt=0.000000, rms=0.527 (0.000%), neg=0, invalid=762 0370: dt=0.150000, rms=0.527 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=762 0371: dt=0.000000, rms=0.527 (0.145%), neg=0, invalid=762 0372: dt=0.000000, rms=0.527 (0.000%), neg=0, invalid=762 0373: dt=0.150000, rms=0.527 (-0.022%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.564, neg=0, invalid=762 0374: dt=0.448000, rms=0.562 (0.289%), neg=0, invalid=762 0375: dt=0.320000, rms=0.562 (0.033%), neg=0, invalid=762 0376: dt=0.320000, rms=0.562 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0377: dt=0.448000, rms=0.562 (0.203%), neg=0, invalid=762 0378: dt=0.192000, rms=0.562 (0.010%), neg=0, invalid=762 0379: dt=0.192000, rms=0.562 (-0.004%), 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=0.514, neg=0, invalid=762 0380: dt=0.448000, rms=0.500 (2.827%), neg=0, invalid=762 0381: dt=0.448000, rms=0.497 (0.570%), neg=0, invalid=762 0382: dt=0.448000, rms=0.495 (0.305%), neg=0, invalid=762 0383: dt=0.448000, rms=0.495 (0.175%), neg=0, invalid=762 0384: dt=0.448000, rms=0.494 (0.122%), neg=0, invalid=762 0385: dt=0.448000, rms=0.494 (0.090%), neg=0, invalid=762 0386: dt=0.448000, rms=0.493 (0.070%), neg=0, invalid=762 0387: dt=0.448000, rms=0.493 (0.051%), neg=0, invalid=762 0388: dt=0.448000, rms=0.493 (0.045%), neg=0, invalid=762 0389: dt=0.448000, rms=0.493 (0.033%), neg=0, invalid=762 0390: dt=0.448000, rms=0.492 (0.060%), neg=0, invalid=762 0391: dt=0.448000, rms=0.492 (0.072%), neg=0, invalid=762 0392: dt=0.448000, rms=0.492 (0.065%), neg=0, invalid=762 0393: dt=0.448000, rms=0.492 (-0.005%), neg=0, invalid=762 0394: dt=0.112000, rms=0.492 (0.001%), neg=0, invalid=762 0395: dt=0.256000, rms=0.492 (0.005%), neg=0, invalid=762 0396: dt=0.448000, rms=0.492 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=762 0397: dt=0.384000, rms=0.486 (1.203%), neg=0, invalid=762 0398: dt=0.384000, rms=0.485 (0.278%), neg=0, invalid=762 0399: dt=0.384000, rms=0.485 (0.097%), neg=0, invalid=762 0400: dt=0.448000, rms=0.484 (0.045%), neg=0, invalid=762 0401: dt=0.448000, rms=0.484 (0.010%), neg=0, invalid=762 0402: dt=0.448000, rms=0.484 (0.019%), neg=0, invalid=762 0403: dt=0.448000, rms=0.484 (-0.001%), 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=0.483, neg=0, invalid=762 0404: dt=0.000000, rms=0.482 (0.175%), neg=0, invalid=762 0405: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0406: dt=129.472000, rms=0.482 (0.193%), neg=0, invalid=762 0407: dt=129.472000, rms=0.482 (0.021%), neg=0, invalid=762 0408: dt=129.472000, rms=0.482 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0409: dt=9.072000, rms=0.482 (0.187%), neg=0, invalid=762 0410: dt=6.480000, rms=0.482 (0.004%), neg=0, invalid=762 0411: dt=6.480000, rms=0.482 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0412: dt=82.944000, rms=0.481 (0.350%), neg=0, invalid=762 0413: dt=36.288000, rms=0.481 (0.089%), neg=0, invalid=762 0414: dt=36.288000, rms=0.481 (0.047%), neg=0, invalid=762 0415: dt=36.288000, rms=0.480 (0.076%), neg=0, invalid=762 0416: dt=36.288000, rms=0.480 (0.088%), neg=0, invalid=762 0417: dt=36.288000, rms=0.479 (0.077%), neg=0, invalid=762 0418: dt=36.288000, rms=0.479 (0.073%), neg=0, invalid=762 0419: dt=124.416000, rms=0.479 (0.046%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0420: dt=11.200000, rms=0.478 (0.363%), neg=0, invalid=762 0421: dt=11.200000, rms=0.478 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0422: dt=11.200000, rms=0.477 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0423: dt=11.200000, rms=0.477 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0424: dt=11.200000, rms=0.477 (-0.049%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0425: dt=30.740984, rms=0.473 (0.979%), neg=0, invalid=762 0426: dt=11.200000, rms=0.472 (0.262%), neg=0, invalid=762 0427: dt=92.207407, rms=0.470 (0.524%), neg=0, invalid=762 0428: dt=11.200000, rms=0.468 (0.309%), neg=0, invalid=762 0429: dt=44.800000, rms=0.467 (0.181%), neg=0, invalid=762 0430: dt=44.800000, rms=0.467 (-0.322%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0431: dt=9.022556, rms=0.467 (0.713%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0432: dt=14.989474, rms=0.465 (0.279%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0433: dt=13.824000, rms=0.465 (0.197%), neg=0, invalid=762 0434: dt=13.824000, rms=0.464 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0435: dt=13.824000, rms=0.463 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0436: dt=13.824000, rms=0.462 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0437: dt=13.824000, rms=0.461 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0438: dt=13.824000, rms=0.460 (0.149%), neg=0, invalid=762 0439: dt=13.824000, rms=0.460 (0.085%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0440: dt=13.824000, rms=0.460 (0.045%), neg=0, invalid=762 0441: dt=10.222222, rms=0.459 (0.095%), neg=0, invalid=762 0442: dt=5.000000, rms=0.459 (0.030%), neg=0, invalid=762 0443: dt=5.000000, rms=0.459 (0.015%), neg=0, invalid=762 0444: dt=5.000000, rms=0.459 (0.005%), neg=0, invalid=762 0445: dt=5.000000, rms=0.459 (0.016%), neg=0, invalid=762 0446: dt=5.000000, rms=0.459 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 0447: dt=14.185075, rms=0.455 (1.003%), neg=0, invalid=762 0448: dt=9.801047, rms=0.454 (0.245%), neg=0, invalid=762 0449: dt=9.801047, rms=0.453 (0.172%), neg=0, invalid=762 0450: dt=9.801047, rms=0.452 (0.189%), neg=0, invalid=762 0451: dt=9.801047, rms=0.452 (0.133%), neg=0, invalid=762 0452: dt=9.801047, rms=0.452 (0.036%), neg=0, invalid=762 0453: dt=9.801047, rms=0.451 (0.099%), neg=0, invalid=762 0454: dt=9.801047, rms=0.451 (0.129%), neg=0, invalid=762 0455: dt=9.801047, rms=0.450 (0.130%), neg=0, invalid=762 0456: dt=9.801047, rms=0.450 (0.094%), neg=0, invalid=762 0457: dt=9.801047, rms=0.449 (0.111%), neg=0, invalid=762 0458: dt=9.801047, rms=0.449 (0.093%), neg=0, invalid=762 0459: dt=6.400000, rms=0.449 (0.057%), neg=0, invalid=762 0460: dt=6.400000, rms=0.448 (0.023%), neg=0, invalid=762 0461: dt=6.400000, rms=0.448 (0.022%), neg=0, invalid=762 0462: dt=6.400000, rms=0.448 (0.014%), 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 0463: dt=0.000000, rms=0.453 (0.190%), neg=0, invalid=762 0464: dt=0.000000, rms=0.453 (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 0465: dt=0.000000, rms=0.453 (0.190%), neg=0, invalid=762 0466: dt=0.000000, rms=0.453 (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 = 747 after 12 iterations, nbhd size=1, neg = 0 0467: dt=1.995590, rms=0.420 (5.868%), neg=0, invalid=762 0468: dt=0.024000, rms=0.420 (0.006%), neg=0, invalid=762 0469: dt=0.024000, rms=0.420 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.421, neg=0, invalid=762 0470: dt=0.096000, rms=0.419 (0.329%), neg=0, invalid=762 0471: dt=0.007000, rms=0.419 (0.001%), neg=0, invalid=762 0472: dt=0.007000, rms=0.419 (0.000%), neg=0, invalid=762 0473: dt=0.007000, rms=0.419 (-0.001%), 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=0.408, neg=0, invalid=762 0474: dt=4.624000, rms=0.408 (0.001%), neg=0, invalid=762 0475: dt=0.361250, rms=0.408 (0.000%), neg=0, invalid=762 0476: dt=0.361250, rms=0.408 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0477: dt=27.744000, rms=0.408 (0.005%), neg=0, invalid=762 0478: dt=8.092000, rms=0.408 (0.000%), neg=0, invalid=762 0479: dt=8.092000, rms=0.408 (0.000%), neg=0, invalid=762 0480: dt=8.092000, rms=0.408 (-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=0.409, neg=0, invalid=762 0481: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0482: dt=36.288000, rms=0.408 (0.035%), neg=0, invalid=762 0483: dt=103.680000, rms=0.408 (0.036%), neg=0, invalid=762 0484: dt=124.416000, rms=0.408 (0.025%), neg=0, invalid=762 0485: dt=124.416000, rms=0.408 (-0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0486: dt=2.800000, rms=0.409 (0.019%), neg=0, invalid=762 0487: dt=2.800000, rms=0.409 (0.006%), neg=0, invalid=762 0488: dt=2.800000, rms=0.409 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0489: dt=86.502283, rms=0.406 (0.557%), neg=0, invalid=762 0490: dt=22.970297, rms=0.406 (0.178%), neg=0, invalid=762 0491: dt=22.970297, rms=0.405 (0.073%), neg=0, invalid=762 0492: dt=22.970297, rms=0.405 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=22.970297, rms=0.404 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0494: dt=22.970297, rms=0.404 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0495: dt=22.970297, rms=0.403 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0496: dt=22.970297, rms=0.403 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0497: dt=22.970297, rms=0.402 (0.107%), neg=0, invalid=762 0498: dt=25.600000, rms=0.402 (0.011%), neg=0, invalid=762 0499: dt=25.600000, rms=0.402 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0500: dt=25.600000, rms=0.402 (0.021%), neg=0, invalid=762 0501: dt=25.600000, rms=0.402 (0.027%), neg=0, invalid=762 0502: dt=25.600000, rms=0.402 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0503: dt=25.600000, rms=0.402 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0504: dt=25.600000, rms=0.402 (0.043%), neg=0, invalid=762 0505: dt=25.600000, rms=0.401 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0506: dt=25.600000, rms=0.401 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0507: dt=25.600000, rms=0.401 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=0, neg = 0 0508: dt=25.600000, rms=0.401 (0.042%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0509: dt=0.000135, rms=0.404 (0.000%), neg=0, invalid=762 0510: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0511: dt=8.450704, rms=0.404 (0.073%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0512: dt=15.652174, rms=0.403 (0.081%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 13 iterations, nbhd size=1, neg = 0 0513: dt=58.448980, rms=0.402 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0514: dt=19.000000, rms=0.402 (0.172%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 5 iterations, nbhd size=0, neg = 0 0515: dt=19.000000, rms=0.402 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 11 iterations, nbhd size=1, neg = 0 0516: dt=19.000000, rms=0.401 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 45 after 20 iterations, nbhd size=1, neg = 0 0517: dt=19.000000, rms=0.401 (0.018%), neg=0, invalid=762 iter 0, gcam->neg = 93 after 16 iterations, nbhd size=1, neg = 0 0518: dt=19.000000, rms=0.401 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 81 after 15 iterations, nbhd size=1, neg = 0 0519: dt=19.000000, rms=0.401 (0.036%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.406, neg=0, invalid=762 0520: dt=0.000050, rms=0.406 (0.000%), neg=0, invalid=762 0521: dt=0.000000, rms=0.406 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=762 0522: dt=0.000000, rms=0.406 (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=0.397, neg=0, invalid=762 iter 0, gcam->neg = 650 after 13 iterations, nbhd size=1, neg = 0 0523: dt=1.280000, rms=0.389 (2.016%), neg=0, invalid=762 0524: dt=0.000015, rms=0.389 (0.000%), neg=0, invalid=762 0525: dt=0.000015, rms=0.389 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=762 0526: dt=0.112000, rms=0.389 (0.093%), neg=0, invalid=762 0527: dt=0.112000, rms=0.389 (0.035%), neg=0, invalid=762 0528: dt=0.112000, rms=0.389 (0.020%), neg=0, invalid=762 0529: dt=0.112000, rms=0.389 (-0.029%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 30 minutes and 30 seconds. mri_ca_register utimesec 9954.389702 mri_ca_register stimesec 8.388724 mri_ca_register ru_maxrss 1342628 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 3579157 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63368 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 3436 mri_ca_register ru_nivcsw 27757 FSRUNTIME@ mri_ca_register 2.5083 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 20:43:33 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-967 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-6.0.0/0051105/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 = 2 == 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 6.14 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 = 0.12842 (10) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (402 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (402 voxels, peak = 9), gca=8.9 gca peak = 0.17677 (13) mri peak = 0.09407 (10) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (250 voxels, overlap=0.422) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (250 voxels, peak = 7), gca=7.2 gca peak = 0.28129 (95) mri peak = 0.09944 (87) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (618 voxels, overlap=0.079) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (618 voxels, peak = 87), gca=86.9 gca peak = 0.16930 (96) mri peak = 0.09299 (89) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (603 voxels, overlap=0.535) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (603 voxels, peak = 88), gca=87.8 gca peak = 0.24553 (55) mri peak = 0.11855 (58) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (575 voxels, overlap=1.004) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (575 voxels, peak = 52), gca=52.0 gca peak = 0.30264 (59) mri peak = 0.08911 (54) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (668 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (668 voxels, peak = 56), gca=55.8 gca peak = 0.07580 (103) mri peak = 0.09635 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38679 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38679 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.09987 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (37237 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (37237 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04919 (55) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (24608 voxels, overlap=0.948) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (24608 voxels, peak = 55), gca=54.8 gca peak = 0.11620 (58) mri peak = 0.05033 (51) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (24622 voxels, overlap=0.918) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (24622 voxels, peak = 53), gca=53.1 gca peak = 0.30970 (66) mri peak = 0.09891 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, peak = 66), gca=66.0 gca peak = 0.15280 (69) mri peak = 0.10693 (69) Left_Caudate (11): linear fit = 0.93 x + 0.0 (849 voxels, overlap=0.512) Left_Caudate (11): linear fit = 0.93 x + 0.0 (849 voxels, peak = 64), gca=63.8 gca peak = 0.13902 (56) mri peak = 0.05194 (55) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15876 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (15876 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.04853 (55) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (17828 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (17828 voxels, peak = 52), gca=52.0 gca peak = 0.16765 (84) mri peak = 0.08307 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4383 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4383 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.08716 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4335 voxels, overlap=0.911) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4335 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.10345 (56) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (415 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (415 voxels, peak = 55), gca=55.0 gca peak = 0.33601 (57) mri peak = 0.10768 (55) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (428 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (428 voxels, peak = 54), gca=53.9 gca peak = 0.11131 (90) mri peak = 0.07890 (82) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3879 voxels, overlap=0.804) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3879 voxels, peak = 86), gca=85.9 gca peak = 0.11793 (83) mri peak = 0.08773 (83) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3993 voxels, overlap=0.974) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3993 voxels, peak = 82), gca=81.8 gca peak = 0.08324 (81) mri peak = 0.09324 (76) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2146 voxels, overlap=0.712) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2146 voxels, peak = 77), gca=76.5 gca peak = 0.10360 (77) mri peak = 0.07948 (72) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2223 voxels, overlap=0.772) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2223 voxels, peak = 72), gca=72.0 gca peak = 0.08424 (78) mri peak = 0.13054 (80) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11036 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11036 voxels, peak = 81), gca=80.7 gca peak = 0.12631 (89) mri peak = 0.08984 (87) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1297 voxels, overlap=0.823) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1297 voxels, peak = 87), gca=86.8 gca peak = 0.14500 (87) mri peak = 0.08968 (86) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1408 voxels, overlap=0.913) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1408 voxels, peak = 85), gca=84.8 gca peak = 0.14975 (24) mri peak = 0.04717 ( 4) gca peak = 0.19357 (14) mri peak = 0.09621 (10) 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 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 0.94 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.50 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.29485 ( 9) mri peak = 0.12842 (10) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (402 voxels, overlap=0.959) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (402 voxels, peak = 9), gca=9.5 gca peak = 0.25357 ( 7) mri peak = 0.09407 (10) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (250 voxels, overlap=0.936) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (250 voxels, peak = 8), gca=7.5 gca peak = 0.26667 (87) mri peak = 0.09944 (87) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (618 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (618 voxels, peak = 86), gca=85.7 gca peak = 0.17947 (88) mri peak = 0.09299 (89) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (603 voxels, overlap=1.006) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (603 voxels, peak = 88), gca=87.6 gca peak = 0.27769 (52) mri peak = 0.11855 (58) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (575 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (575 voxels, peak = 53), gca=52.8 gca peak = 0.30423 (53) mri peak = 0.08911 (54) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (668 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (668 voxels, peak = 55), gca=55.4 gca peak = 0.07771 (104) mri peak = 0.09635 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38679 voxels, overlap=0.753) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38679 voxels, peak = 104), gca=104.0 gca peak = 0.07820 (106) mri peak = 0.09987 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37237 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37237 voxels, peak = 106), gca=106.0 gca peak = 0.10313 (55) mri peak = 0.04919 (55) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24608 voxels, overlap=0.996) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24608 voxels, peak = 54), gca=54.2 gca peak = 0.12643 (53) mri peak = 0.05033 (51) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (24622 voxels, overlap=0.986) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (24622 voxels, peak = 53), gca=53.0 gca peak = 0.30965 (66) mri peak = 0.09891 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.00 x + 0.0 (868 voxels, peak = 66), gca=66.0 gca peak = 0.13200 (64) mri peak = 0.10693 (69) Left_Caudate (11): linear fit = 0.99 x + 0.0 (849 voxels, overlap=0.990) Left_Caudate (11): linear fit = 0.99 x + 0.0 (849 voxels, peak = 63), gca=63.0 gca peak = 0.13344 (57) mri peak = 0.05194 (55) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (15876 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (15876 voxels, peak = 55), gca=55.0 gca peak = 0.15539 (52) mri peak = 0.04853 (55) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17828 voxels, overlap=0.996) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17828 voxels, peak = 54), gca=54.3 gca peak = 0.15873 (90) mri peak = 0.08307 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4383 voxels, overlap=0.958) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4383 voxels, peak = 91), gca=91.3 gca peak = 0.18381 (87) mri peak = 0.08716 (85) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4335 voxels, overlap=0.980) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4335 voxels, peak = 86), gca=85.7 gca peak = 0.29815 (55) mri peak = 0.10345 (56) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (415 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (415 voxels, peak = 55), gca=55.0 gca peak = 0.41931 (54) mri peak = 0.10768 (55) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (428 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (428 voxels, peak = 54), gca=54.0 gca peak = 0.11467 (86) mri peak = 0.07890 (82) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3879 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3879 voxels, peak = 85), gca=84.7 gca peak = 0.10564 (79) mri peak = 0.08773 (83) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3993 voxels, overlap=0.943) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3993 voxels, peak = 80), gca=80.2 gca peak = 0.09401 (78) mri peak = 0.09324 (76) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2146 voxels, overlap=0.912) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2146 voxels, peak = 78), gca=78.0 gca peak = 0.09691 (72) mri peak = 0.07948 (72) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2223 voxels, overlap=0.994) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2223 voxels, peak = 73), gca=73.1 gca peak = 0.08837 (81) mri peak = 0.13054 (80) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11036 voxels, overlap=0.621) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11036 voxels, peak = 82), gca=82.2 gca peak = 0.13258 (87) mri peak = 0.08984 (87) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1297 voxels, overlap=0.791) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1297 voxels, peak = 87), gca=86.6 gca peak = 0.14341 (83) mri peak = 0.08968 (86) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1408 voxels, overlap=0.877) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1408 voxels, peak = 83), gca=82.6 gca peak = 0.29623 (13) mri peak = 0.04717 ( 4) gca peak = 0.31719 ( 7) mri peak = 0.09621 (10) gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18199 (30) gca peak Left_Thalamus = 1.00000 (89) gca peak Third_Ventricle = 0.29623 (13) gca peak Fourth_Ventricle = 0.31719 ( 7) gca peak CSF = 0.39966 (18) gca peak Left_Accumbens_area = 0.54630 (57) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.76046 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.26998 (22) gca peak Right_Accumbens_area = 0.42997 (65) gca peak Right_vessel = 0.82280 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.89470 (16) gca peak WM_hypointensities = 0.07201 (78) gca peak non_WM_hypointensities = 0.09744 (44) gca peak Optic_Chiasm = 0.71107 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.07 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 55681 voxels changed in iteration 0 of unlikely voxel relabeling 108 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 27832 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 346 hippocampal voxels changed. 2 amygdala voxels changed. pass 1: 63045 changed. image ll: -2.093, PF=0.500 pass 2: 17237 changed. image ll: -2.092, PF=0.500 pass 3: 5368 changed. pass 4: 1904 changed. 31194 voxels changed in iteration 0 of unlikely voxel relabeling 162 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4996 voxels changed in iteration 0 of unlikely voxel relabeling 45 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4814 voxels changed in iteration 0 of unlikely voxel relabeling 47 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 3848 voxels changed in iteration 0 of unlikely voxel relabeling 17 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 3103.937129 mri_ca_label stimesec 1.551764 mri_ca_label ru_maxrss 2103344 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 649072 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 63360 mri_ca_label ru_oublock 448 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 282 mri_ca_label ru_nivcsw 6638 auto-labeling took 51 minutes and 4 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/transforms/cc_up.lta 0051105 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-6.0.0/0051105/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/norm.mgz 50632 voxels in left wm, 33313 in right wm, xrange [120, 130] searching rotation angles z=[-4 10], y=[-6 8] searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.6 global minimum found at slice 123.6, rotations (1.27, 2.80) final transformation (x=123.6, yr=1.265, zr=2.804): 0.99856 -0.04892 0.02206 6.94757; 0.04891 0.99880 0.00108 23.95334; -0.02209 0.00000 0.99976 19.75628; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 98 111 eigenvectors: 0.00005 -0.00418 0.99999; -0.20966 -0.97777 -0.00407; 0.97777 -0.20966 -0.00093; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 21:35:29 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 21:35:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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... 1100 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 110 gm peak at 60 (60), valley at 20 (20) csf peak at 30, setting threshold to 50 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 60 (60), valley at 19 (19) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 12 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 21:38:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1459687 voxels in mask (pct= 8.70) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 21:38:44 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 (106.0): 106.4 +- 5.3 [79.0 --> 125.0] GM (68.0) : 66.6 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 76.2 setting top of gray matter range to 85.9 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... 6852 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5292 filled 3265 bright non-wm voxels segmented. 3056 diagonally connected voxels added... white matter segmentation took 1.4 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... 88 voxels added to wm to prevent paths from MTL structures to cortex 2320 additional wm voxels added 0 additional wm voxels added SEG EDIT: 36336 voxels turned on, 33511 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 116 new 116 115,126,128 old 116 new 116 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 19 found - 19 modified | TOTAL: 19 pass 2 (xy+): 0 found - 19 modified | TOTAL: 19 pass 1 (xy-): 24 found - 24 modified | TOTAL: 43 pass 2 (xy-): 0 found - 24 modified | TOTAL: 43 pass 1 (yz+): 28 found - 28 modified | TOTAL: 71 pass 2 (yz+): 0 found - 28 modified | TOTAL: 71 pass 1 (yz-): 24 found - 24 modified | TOTAL: 95 pass 2 (yz-): 0 found - 24 modified | TOTAL: 95 pass 1 (xz+): 26 found - 26 modified | TOTAL: 121 pass 2 (xz+): 0 found - 26 modified | TOTAL: 121 pass 1 (xz-): 18 found - 18 modified | TOTAL: 139 pass 2 (xz-): 0 found - 18 modified | TOTAL: 139 Iteration Number : 1 pass 1 (+++): 19 found - 19 modified | TOTAL: 19 pass 2 (+++): 0 found - 19 modified | TOTAL: 19 pass 1 (+++): 34 found - 34 modified | TOTAL: 53 pass 2 (+++): 0 found - 34 modified | TOTAL: 53 pass 1 (+++): 26 found - 26 modified | TOTAL: 79 pass 2 (+++): 0 found - 26 modified | TOTAL: 79 pass 1 (+++): 11 found - 11 modified | TOTAL: 90 pass 2 (+++): 0 found - 11 modified | TOTAL: 90 Iteration Number : 1 pass 1 (++): 129 found - 129 modified | TOTAL: 129 pass 2 (++): 0 found - 129 modified | TOTAL: 129 pass 1 (+-): 120 found - 120 modified | TOTAL: 249 pass 2 (+-): 0 found - 120 modified | TOTAL: 249 pass 1 (--): 134 found - 134 modified | TOTAL: 383 pass 2 (--): 0 found - 134 modified | TOTAL: 383 pass 1 (-+): 115 found - 115 modified | TOTAL: 498 pass 2 (-+): 0 found - 115 modified | TOTAL: 498 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 2 found - 2 modified | TOTAL: 6 pass 2 (xy-): 0 found - 2 modified | TOTAL: 6 pass 1 (yz+): 2 found - 2 modified | TOTAL: 8 pass 2 (yz+): 0 found - 2 modified | TOTAL: 8 pass 1 (yz-): 2 found - 2 modified | TOTAL: 10 pass 2 (yz-): 0 found - 2 modified | TOTAL: 10 pass 1 (xz+): 9 found - 9 modified | TOTAL: 19 pass 2 (xz+): 0 found - 9 modified | TOTAL: 19 pass 1 (xz-): 7 found - 7 modified | TOTAL: 26 pass 2 (xz-): 0 found - 7 modified | TOTAL: 26 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 1 found - 1 modified | TOTAL: 7 pass 2 (+++): 0 found - 1 modified | TOTAL: 7 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 2 found - 2 modified | TOTAL: 8 pass 2 (-+): 0 found - 2 modified | TOTAL: 8 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 768 (out of 504614: 0.152196) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 21:40:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 1.03374 -0.04445 0.02053 1.61642; 0.02912 1.07990 0.39074 -49.35634; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03374 -0.04445 0.02053 1.61642; 0.02912 1.07990 0.39074 -49.35634; -0.03759 -0.39978 1.02050 41.71447; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1309 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) no need to search using seed (126, 124, 151), TAL = (2.0, 23.0, 4.0) talairach voxel to voxel transform 0.96546 0.02851 -0.03034 1.11210; -0.03407 0.81004 -0.30947 52.94506; 0.02222 0.31838 0.85756 -20.09424; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 124, 151) --> (2.0, 23.0, 4.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (2.00, 23.00, 4.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 4.00) SRC: (104.34, 102.98, 151.28) search lh wm seed point around talairach space (-16.00, 23.00, 4.00), SRC: (139.09, 101.75, 152.08) 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 Sat Oct 7 21:41:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 1 found - 1 modified | TOTAL: 6 pass 2 (xy-): 0 found - 1 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 modified | TOTAL: 12 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 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 : 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 = 17 (out of 242126: 0.007021) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1238 vertices, 1351 faces slice 60: 9362 vertices, 9770 faces slice 70: 22016 vertices, 22452 faces slice 80: 34953 vertices, 35432 faces slice 90: 48745 vertices, 49218 faces slice 100: 61229 vertices, 61689 faces slice 110: 73470 vertices, 73883 faces slice 120: 85099 vertices, 85558 faces slice 130: 95678 vertices, 96099 faces slice 140: 106091 vertices, 106478 faces slice 150: 115147 vertices, 115478 faces slice 160: 123658 vertices, 123997 faces slice 170: 129909 vertices, 130174 faces slice 180: 134975 vertices, 135213 faces slice 190: 138369 vertices, 138512 faces slice 200: 138684 vertices, 138762 faces slice 210: 138684 vertices, 138762 faces slice 220: 138684 vertices, 138762 faces slice 230: 138684 vertices, 138762 faces slice 240: 138684 vertices, 138762 faces slice 250: 138684 vertices, 138762 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... 138684 voxel in cpt #1: X=-78 [v=138684,e=416286,f=277524] located at (-23.815098, -19.036688, 21.929897) For the whole surface: X=-78 [v=138684,e=416286,f=277524] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 21:41:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 4 found - 4 modified | TOTAL: 6 pass 2 (yz+): 0 found - 4 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 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 = 11 (out of 241850: 0.004548) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1068 vertices, 1192 faces slice 60: 8981 vertices, 9368 faces slice 70: 21165 vertices, 21643 faces slice 80: 35222 vertices, 35746 faces slice 90: 48699 vertices, 49160 faces slice 100: 60819 vertices, 61255 faces slice 110: 72468 vertices, 72869 faces slice 120: 84202 vertices, 84618 faces slice 130: 94838 vertices, 95257 faces slice 140: 104834 vertices, 105199 faces slice 150: 114025 vertices, 114368 faces slice 160: 122577 vertices, 122889 faces slice 170: 128745 vertices, 129017 faces slice 180: 134369 vertices, 134593 faces slice 190: 137582 vertices, 137674 faces slice 200: 137638 vertices, 137700 faces slice 210: 137638 vertices, 137700 faces slice 220: 137638 vertices, 137700 faces slice 230: 137638 vertices, 137700 faces slice 240: 137638 vertices, 137700 faces slice 250: 137638 vertices, 137700 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... 137638 voxel in cpt #1: X=-62 [v=137638,e=413100,f=275400] located at (31.852715, -18.958689, 20.307655) For the whole surface: X=-62 [v=137638,e=413100,f=275400] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 21:41:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 21:41:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 6099 of (6099 6102) to complete... Waiting for PID 6102 of (6099 6102) 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 (6099 6102) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 21:41:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 21:41:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 6145 of (6145 6148) to complete... Waiting for PID 6148 of (6145 6148) 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 = 45.3 mm, total surface area = 71767 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.042 (target=0.015) step 055: RMS=0.041 (target=0.015) step 060: RMS=0.041 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.777496 mris_inflate stimesec 0.106983 mris_inflate ru_maxrss 202956 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29724 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9776 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2165 mris_inflate ru_nivcsw 3521 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.1 mm, total surface area = 71194 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.161 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.055 (target=0.015) step 035: RMS=0.050 (target=0.015) step 040: RMS=0.048 (target=0.015) step 045: RMS=0.046 (target=0.015) step 050: RMS=0.045 (target=0.015) step 055: RMS=0.044 (target=0.015) step 060: RMS=0.044 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.528534 mris_inflate stimesec 0.103984 mris_inflate ru_maxrss 201304 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29310 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2143 mris_inflate ru_nivcsw 3269 PIDs (6145 6148) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 21:42:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 21:42:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 6215 of (6215 6218) to complete... Waiting for PID 6218 of (6215 6218) 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 0.98 +- 0.59 (0.00-->8.45) (max @ vno 103620 --> 103638) face area 0.03 +- 0.04 (-0.40-->0.78) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.336... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.987, avgs=0 005/300: dt: 0.9000, rms radial error=174.731, avgs=0 010/300: dt: 0.9000, rms radial error=174.181, avgs=0 015/300: dt: 0.9000, rms radial error=173.459, avgs=0 020/300: dt: 0.9000, rms radial error=172.636, avgs=0 025/300: dt: 0.9000, rms radial error=171.754, avgs=0 030/300: dt: 0.9000, rms radial error=170.840, avgs=0 035/300: dt: 0.9000, rms radial error=169.908, avgs=0 040/300: dt: 0.9000, rms radial error=168.967, avgs=0 045/300: dt: 0.9000, rms radial error=168.022, avgs=0 050/300: dt: 0.9000, rms radial error=167.077, avgs=0 055/300: dt: 0.9000, rms radial error=166.134, avgs=0 060/300: dt: 0.9000, rms radial error=165.193, avgs=0 065/300: dt: 0.9000, rms radial error=164.257, avgs=0 070/300: dt: 0.9000, rms radial error=163.324, avgs=0 075/300: dt: 0.9000, rms radial error=162.397, avgs=0 080/300: dt: 0.9000, rms radial error=161.477, avgs=0 085/300: dt: 0.9000, rms radial error=160.565, avgs=0 090/300: dt: 0.9000, rms radial error=159.659, avgs=0 095/300: dt: 0.9000, rms radial error=158.758, avgs=0 100/300: dt: 0.9000, rms radial error=157.862, avgs=0 105/300: dt: 0.9000, rms radial error=156.971, avgs=0 110/300: dt: 0.9000, rms radial error=156.085, avgs=0 115/300: dt: 0.9000, rms radial error=155.203, avgs=0 120/300: dt: 0.9000, rms radial error=154.328, avgs=0 125/300: dt: 0.9000, rms radial error=153.458, avgs=0 130/300: dt: 0.9000, rms radial error=152.592, avgs=0 135/300: dt: 0.9000, rms radial error=151.731, avgs=0 140/300: dt: 0.9000, rms radial error=150.874, avgs=0 145/300: dt: 0.9000, rms radial error=150.023, avgs=0 150/300: dt: 0.9000, rms radial error=149.177, avgs=0 155/300: dt: 0.9000, rms radial error=148.335, avgs=0 160/300: dt: 0.9000, rms radial error=147.498, avgs=0 165/300: dt: 0.9000, rms radial error=146.665, avgs=0 170/300: dt: 0.9000, rms radial error=145.837, avgs=0 175/300: dt: 0.9000, rms radial error=145.015, avgs=0 180/300: dt: 0.9000, rms radial error=144.197, avgs=0 185/300: dt: 0.9000, rms radial error=143.385, avgs=0 190/300: dt: 0.9000, rms radial error=142.576, avgs=0 195/300: dt: 0.9000, rms radial error=141.772, avgs=0 200/300: dt: 0.9000, rms radial error=140.973, avgs=0 205/300: dt: 0.9000, rms radial error=140.178, avgs=0 210/300: dt: 0.9000, rms radial error=139.387, avgs=0 215/300: dt: 0.9000, rms radial error=138.601, avgs=0 220/300: dt: 0.9000, rms radial error=137.819, avgs=0 225/300: dt: 0.9000, rms radial error=137.041, avgs=0 230/300: dt: 0.9000, rms radial error=136.268, avgs=0 235/300: dt: 0.9000, rms radial error=135.499, avgs=0 240/300: dt: 0.9000, rms radial error=134.735, avgs=0 245/300: dt: 0.9000, rms radial error=133.975, avgs=0 250/300: dt: 0.9000, rms radial error=133.218, avgs=0 255/300: dt: 0.9000, rms radial error=132.467, avgs=0 260/300: dt: 0.9000, rms radial error=131.719, avgs=0 265/300: dt: 0.9000, rms radial error=130.975, avgs=0 270/300: dt: 0.9000, rms radial error=130.236, avgs=0 275/300: dt: 0.9000, rms radial error=129.501, avgs=0 280/300: dt: 0.9000, rms radial error=128.770, avgs=0 285/300: dt: 0.9000, rms radial error=128.044, avgs=0 290/300: dt: 0.9000, rms radial error=127.319, avgs=0 295/300: dt: 0.9000, rms radial error=126.601, avgs=0 300/300: dt: 0.9000, rms radial error=125.888, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15913.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2600.95 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 246.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00178 epoch 4 (K=640.0), pass 1, starting sse = 17.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00302 final distance error %26.28 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 238.110801 mris_sphere stimesec 0.176973 mris_sphere ru_maxrss 203164 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 29263 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9800 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 10207 mris_sphere ru_nivcsw 17488 FSRUNTIME@ mris_sphere 0.0662 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 0.99 +- 0.59 (0.00-->8.37) (max @ vno 101870 --> 101871) face area 0.03 +- 0.04 (-0.25-->0.68) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.341... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.740, avgs=0 005/300: dt: 0.9000, rms radial error=174.483, avgs=0 010/300: dt: 0.9000, rms radial error=173.931, avgs=0 015/300: dt: 0.9000, rms radial error=173.211, avgs=0 020/300: dt: 0.9000, rms radial error=172.390, avgs=0 025/300: dt: 0.9000, rms radial error=171.512, avgs=0 030/300: dt: 0.9000, rms radial error=170.601, avgs=0 035/300: dt: 0.9000, rms radial error=169.673, avgs=0 040/300: dt: 0.9000, rms radial error=168.736, avgs=0 045/300: dt: 0.9000, rms radial error=167.797, avgs=0 050/300: dt: 0.9000, rms radial error=166.857, avgs=0 055/300: dt: 0.9000, rms radial error=165.918, avgs=0 060/300: dt: 0.9000, rms radial error=164.982, avgs=0 065/300: dt: 0.9000, rms radial error=164.050, avgs=0 070/300: dt: 0.9000, rms radial error=163.129, avgs=0 075/300: dt: 0.9000, rms radial error=162.213, avgs=0 080/300: dt: 0.9000, rms radial error=161.302, avgs=0 085/300: dt: 0.9000, rms radial error=160.396, avgs=0 090/300: dt: 0.9000, rms radial error=159.496, avgs=0 095/300: dt: 0.9000, rms radial error=158.603, avgs=0 100/300: dt: 0.9000, rms radial error=157.715, avgs=0 105/300: dt: 0.9000, rms radial error=156.831, avgs=0 110/300: dt: 0.9000, rms radial error=155.952, avgs=0 115/300: dt: 0.9000, rms radial error=155.078, avgs=0 120/300: dt: 0.9000, rms radial error=154.208, avgs=0 125/300: dt: 0.9000, rms radial error=153.343, avgs=0 130/300: dt: 0.9000, rms radial error=152.483, avgs=0 135/300: dt: 0.9000, rms radial error=151.629, avgs=0 140/300: dt: 0.9000, rms radial error=150.780, avgs=0 145/300: dt: 0.9000, rms radial error=149.935, avgs=0 150/300: dt: 0.9000, rms radial error=149.095, avgs=0 155/300: dt: 0.9000, rms radial error=148.259, avgs=0 160/300: dt: 0.9000, rms radial error=147.428, avgs=0 165/300: dt: 0.9000, rms radial error=146.601, avgs=0 170/300: dt: 0.9000, rms radial error=145.779, avgs=0 175/300: dt: 0.9000, rms radial error=144.961, avgs=0 180/300: dt: 0.9000, rms radial error=144.148, avgs=0 185/300: dt: 0.9000, rms radial error=143.339, avgs=0 190/300: dt: 0.9000, rms radial error=142.535, avgs=0 195/300: dt: 0.9000, rms radial error=141.735, avgs=0 200/300: dt: 0.9000, rms radial error=140.939, avgs=0 205/300: dt: 0.9000, rms radial error=140.147, avgs=0 210/300: dt: 0.9000, rms radial error=139.360, avgs=0 215/300: dt: 0.9000, rms radial error=138.577, avgs=0 220/300: dt: 0.9000, rms radial error=137.799, avgs=0 225/300: dt: 0.9000, rms radial error=137.025, avgs=0 230/300: dt: 0.9000, rms radial error=136.256, avgs=0 235/300: dt: 0.9000, rms radial error=135.491, avgs=0 240/300: dt: 0.9000, rms radial error=134.730, avgs=0 245/300: dt: 0.9000, rms radial error=133.973, avgs=0 250/300: dt: 0.9000, rms radial error=133.221, avgs=0 255/300: dt: 0.9000, rms radial error=132.473, avgs=0 260/300: dt: 0.9000, rms radial error=131.730, avgs=0 265/300: dt: 0.9000, rms radial error=130.990, avgs=0 270/300: dt: 0.9000, rms radial error=130.255, avgs=0 275/300: dt: 0.9000, rms radial error=129.524, avgs=0 280/300: dt: 0.9000, rms radial error=128.796, avgs=0 285/300: dt: 0.9000, rms radial error=128.073, avgs=0 290/300: dt: 0.9000, rms radial error=127.354, avgs=0 295/300: dt: 0.9000, rms radial error=126.639, avgs=0 300/300: dt: 0.9000, rms radial error=125.927, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15691.36 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2517.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 233.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00207 epoch 4 (K=640.0), pass 1, starting sse = 16.03 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00253 final distance error %25.81 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 237.648871 mris_sphere stimesec 0.198969 mris_sphere ru_maxrss 201500 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 29364 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9728 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7734 mris_sphere ru_nivcsw 19187 FSRUNTIME@ mris_sphere 0.0661 hours 1 threads PIDs (6215 6218) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 21:46:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 21:46:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 21:46:29 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 lh #@# Fix Topology rh Sat Oct 7 21:46:29 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 rh Waiting for PID 6397 of (6397 6400) to complete... Waiting for PID 6400 of (6397 6400) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 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=-78 (nv=138684, nf=277524, ne=416286, g=40) 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 13 iterations marking ambiguous vertices... 4846 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 41 into 40 43 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5727 (-4.7863) -vertex loglikelihood: -6.5155 (-3.2577) -normal dot loglikelihood: -3.6289 (-3.6289) -quad curv loglikelihood: -6.6108 (-3.3054) Total Loglikelihood : -26.3279 CORRECTING DEFECT 0 (vertices=46, convex hull=76, v0=497) After retessellation of defect 0 (v0=497), euler #=-41 (135635,405446,269770) : difference with theory (-40) = 1 CORRECTING DEFECT 1 (vertices=45, convex hull=98, v0=1730) After retessellation of defect 1 (v0=1730), euler #=-40 (135659,405557,269858) : difference with theory (-39) = 1 CORRECTING DEFECT 2 (vertices=241, convex hull=205, v0=2156) After retessellation of defect 2 (v0=2156), euler #=-39 (135754,405941,270148) : difference with theory (-38) = 1 CORRECTING DEFECT 3 (vertices=92, convex hull=129, v0=12686) After retessellation of defect 3 (v0=12686), euler #=-38 (135815,406179,270326) : difference with theory (-37) = 1 CORRECTING DEFECT 4 (vertices=58, convex hull=114, v0=14162) After retessellation of defect 4 (v0=14162), euler #=-37 (135844,406319,270438) : difference with theory (-36) = 1 CORRECTING DEFECT 5 (vertices=25, convex hull=45, v0=36340) After retessellation of defect 5 (v0=36340), euler #=-36 (135859,406380,270485) : difference with theory (-35) = 1 CORRECTING DEFECT 6 (vertices=33, convex hull=68, v0=37580) After retessellation of defect 6 (v0=37580), euler #=-35 (135873,406449,270541) : difference with theory (-34) = 1 CORRECTING DEFECT 7 (vertices=68, convex hull=103, v0=44028) After retessellation of defect 7 (v0=44028), euler #=-34 (135906,406592,270652) : difference with theory (-33) = 1 CORRECTING DEFECT 8 (vertices=9, convex hull=39, v0=46769) After retessellation of defect 8 (v0=46769), euler #=-33 (135907,406606,270666) : difference with theory (-32) = 1 CORRECTING DEFECT 9 (vertices=47, convex hull=69, v0=47480) After retessellation of defect 9 (v0=47480), euler #=-32 (135924,406686,270730) : difference with theory (-31) = 1 CORRECTING DEFECT 10 (vertices=97, convex hull=87, v0=49502) After retessellation of defect 10 (v0=49502), euler #=-31 (135933,406749,270785) : difference with theory (-30) = 1 CORRECTING DEFECT 11 (vertices=66, convex hull=100, v0=61027) After retessellation of defect 11 (v0=61027), euler #=-30 (135978,406929,270921) : difference with theory (-29) = 1 CORRECTING DEFECT 12 (vertices=97, convex hull=86, v0=61858) After retessellation of defect 12 (v0=61858), euler #=-29 (135995,407017,270993) : difference with theory (-28) = 1 CORRECTING DEFECT 13 (vertices=87, convex hull=63, v0=61887) After retessellation of defect 13 (v0=61887), euler #=-28 (136004,407068,271036) : difference with theory (-27) = 1 CORRECTING DEFECT 14 (vertices=290, convex hull=347, v0=67015) After retessellation of defect 14 (v0=67015), euler #=-27 (136160,407708,271521) : difference with theory (-26) = 1 CORRECTING DEFECT 15 (vertices=32, convex hull=61, v0=75228) After retessellation of defect 15 (v0=75228), euler #=-26 (136176,407781,271579) : difference with theory (-25) = 1 CORRECTING DEFECT 16 (vertices=34, convex hull=40, v0=79035) After retessellation of defect 16 (v0=79035), euler #=-25 (136181,407810,271604) : difference with theory (-24) = 1 CORRECTING DEFECT 17 (vertices=110, convex hull=65, v0=81174) After retessellation of defect 17 (v0=81174), euler #=-24 (136206,407918,271688) : difference with theory (-23) = 1 CORRECTING DEFECT 18 (vertices=9, convex hull=26, v0=86008) After retessellation of defect 18 (v0=86008), euler #=-23 (136208,407935,271704) : difference with theory (-22) = 1 CORRECTING DEFECT 19 (vertices=29, convex hull=22, v0=93331) After retessellation of defect 19 (v0=93331), euler #=-22 (136211,407951,271718) : difference with theory (-21) = 1 CORRECTING DEFECT 20 (vertices=32, convex hull=32, v0=101354) After retessellation of defect 20 (v0=101354), euler #=-21 (136215,407974,271738) : difference with theory (-20) = 1 CORRECTING DEFECT 21 (vertices=31, convex hull=49, v0=102544) After retessellation of defect 21 (v0=102544), euler #=-20 (136227,408029,271782) : difference with theory (-19) = 1 CORRECTING DEFECT 22 (vertices=93, convex hull=78, v0=103701) After retessellation of defect 22 (v0=103701), euler #=-19 (136231,408085,271835) : difference with theory (-18) = 1 CORRECTING DEFECT 23 (vertices=213, convex hull=217, v0=105800) After retessellation of defect 23 (v0=105800), euler #=-18 (136296,408381,272067) : difference with theory (-17) = 1 CORRECTING DEFECT 24 (vertices=14, convex hull=18, v0=107650) After retessellation of defect 24 (v0=107650), euler #=-17 (136298,408392,272077) : difference with theory (-16) = 1 CORRECTING DEFECT 25 (vertices=16, convex hull=31, v0=108724) After retessellation of defect 25 (v0=108724), euler #=-16 (136299,408402,272087) : difference with theory (-15) = 1 CORRECTING DEFECT 26 (vertices=16, convex hull=32, v0=111448) After retessellation of defect 26 (v0=111448), euler #=-15 (136300,408417,272102) : difference with theory (-14) = 1 CORRECTING DEFECT 27 (vertices=43, convex hull=101, v0=112443) After retessellation of defect 27 (v0=112443), euler #=-14 (136320,408524,272190) : difference with theory (-13) = 1 CORRECTING DEFECT 28 (vertices=11, convex hull=19, v0=113114) After retessellation of defect 28 (v0=113114), euler #=-13 (136321,408535,272201) : difference with theory (-12) = 1 CORRECTING DEFECT 29 (vertices=8, convex hull=24, v0=114683) After retessellation of defect 29 (v0=114683), euler #=-12 (136323,408548,272213) : difference with theory (-11) = 1 CORRECTING DEFECT 30 (vertices=25, convex hull=47, v0=115537) After retessellation of defect 30 (v0=115537), euler #=-11 (136333,408596,272252) : difference with theory (-10) = 1 CORRECTING DEFECT 31 (vertices=450, convex hull=116, v0=116379) After retessellation of defect 31 (v0=116379), euler #=-10 (136354,408709,272345) : difference with theory (-9) = 1 CORRECTING DEFECT 32 (vertices=31, convex hull=72, v0=117738) After retessellation of defect 32 (v0=117738), euler #=-9 (136376,408804,272419) : difference with theory (-8) = 1 CORRECTING DEFECT 33 (vertices=81, convex hull=63, v0=118055) After retessellation of defect 33 (v0=118055), euler #=-8 (136392,408874,272474) : difference with theory (-7) = 1 CORRECTING DEFECT 34 (vertices=194, convex hull=193, v0=118285) normal vector of length zero at vertex 138286 with 3 faces normal vector of length zero at vertex 138286 with 3 faces normal vector of length zero at vertex 138286 with 3 faces normal vector of length zero at vertex 138286 with 3 faces normal vector of length zero at vertex 138286 with 3 faces After retessellation of defect 34 (v0=118285), euler #=-7 (136466,409191,272718) : difference with theory (-6) = 1 CORRECTING DEFECT 35 (vertices=50, convex hull=99, v0=118608) After retessellation of defect 35 (v0=118608), euler #=-6 (136491,409309,272812) : difference with theory (-5) = 1 CORRECTING DEFECT 36 (vertices=34, convex hull=59, v0=119337) After retessellation of defect 36 (v0=119337), euler #=-5 (136500,409358,272853) : difference with theory (-4) = 1 CORRECTING DEFECT 37 (vertices=66, convex hull=88, v0=121052) After retessellation of defect 37 (v0=121052), euler #=-4 (136519,409452,272929) : difference with theory (-3) = 1 CORRECTING DEFECT 38 (vertices=16, convex hull=21, v0=121517) After retessellation of defect 38 (v0=121517), euler #=-3 (136522,409468,272943) : difference with theory (-2) = 1 CORRECTING DEFECT 39 (vertices=5, convex hull=26, v0=122815) After retessellation of defect 39 (v0=122815), euler #=-2 (136523,409477,272952) : difference with theory (-1) = 1 CORRECTING DEFECT 40 (vertices=80, convex hull=106, v0=133541) After retessellation of defect 40 (v0=133541), euler #=0 (136542,409582,273040) : difference with theory (0) = 0 CORRECTING DEFECT 41 (vertices=12, convex hull=25, v0=136303) After retessellation of defect 41 (v0=136303), euler #=1 (136544,409597,273054) : difference with theory (1) = 0 CORRECTING DEFECT 42 (vertices=39, convex hull=73, v0=137655) After retessellation of defect 42 (v0=137655), euler #=2 (136564,409686,273124) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.03-->7.96) (max @ vno 70942 --> 74415) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.03-->7.96) (max @ vno 70942 --> 74415) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 155 mutations (34.0%), 301 crossovers (66.0%), 245 vertices were eliminated building final representation... 2120 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136564, nf=273124, ne=409686, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.6 minutes 0 defective edges removing intersecting faces 000: 329 intersecting 001: 17 intersecting mris_fix_topology utimesec 1595.232487 mris_fix_topology stimesec 0.311952 mris_fix_topology ru_maxrss 436208 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55082 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 9760 mris_fix_topology ru_oublock 13104 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 497 mris_fix_topology ru_nivcsw 4681 FSRUNTIME@ mris_fix_topology lh 0.4431 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051105 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-62 (nv=137638, nf=275400, ne=413100, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 4605 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 16 -merging segment 28 into 26 42 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6102 (-4.8051) -vertex loglikelihood: -6.5262 (-3.2631) -normal dot loglikelihood: -3.6026 (-3.6026) -quad curv loglikelihood: -6.6157 (-3.3078) Total Loglikelihood : -26.3547 CORRECTING DEFECT 0 (vertices=159, convex hull=152, v0=2016) After retessellation of defect 0 (v0=2016), euler #=-39 (134820,403252,268393) : difference with theory (-39) = 0 CORRECTING DEFECT 1 (vertices=60, convex hull=98, v0=4183) After retessellation of defect 1 (v0=4183), euler #=-38 (134854,403398,268506) : difference with theory (-38) = 0 CORRECTING DEFECT 2 (vertices=15, convex hull=69, v0=5121) After retessellation of defect 2 (v0=5121), euler #=-37 (134861,403443,268545) : difference with theory (-37) = 0 CORRECTING DEFECT 3 (vertices=7, convex hull=22, v0=12108) After retessellation of defect 3 (v0=12108), euler #=-36 (134862,403452,268554) : difference with theory (-36) = 0 CORRECTING DEFECT 4 (vertices=46, convex hull=101, v0=14822) After retessellation of defect 4 (v0=14822), euler #=-35 (134889,403577,268653) : difference with theory (-35) = 0 CORRECTING DEFECT 5 (vertices=28, convex hull=64, v0=15776) After retessellation of defect 5 (v0=15776), euler #=-34 (134900,403632,268698) : difference with theory (-34) = 0 CORRECTING DEFECT 6 (vertices=236, convex hull=168, v0=18443) After retessellation of defect 6 (v0=18443), euler #=-33 (134959,403892,268900) : difference with theory (-33) = 0 CORRECTING DEFECT 7 (vertices=28, convex hull=61, v0=29150) After retessellation of defect 7 (v0=29150), euler #=-32 (134971,403951,268948) : difference with theory (-32) = 0 CORRECTING DEFECT 8 (vertices=50, convex hull=24, v0=33624) After retessellation of defect 8 (v0=33624), euler #=-31 (134980,403985,268974) : difference with theory (-31) = 0 CORRECTING DEFECT 9 (vertices=37, convex hull=72, v0=38034) After retessellation of defect 9 (v0=38034), euler #=-30 (134996,404065,269039) : difference with theory (-30) = 0 CORRECTING DEFECT 10 (vertices=39, convex hull=74, v0=39026) After retessellation of defect 10 (v0=39026), euler #=-29 (135017,404158,269112) : difference with theory (-29) = 0 CORRECTING DEFECT 11 (vertices=50, convex hull=72, v0=39500) After retessellation of defect 11 (v0=39500), euler #=-28 (135036,404247,269183) : difference with theory (-28) = 0 CORRECTING DEFECT 12 (vertices=35, convex hull=65, v0=43096) After retessellation of defect 12 (v0=43096), euler #=-27 (135052,404326,269247) : difference with theory (-27) = 0 CORRECTING DEFECT 13 (vertices=18, convex hull=22, v0=53503) After retessellation of defect 13 (v0=53503), euler #=-26 (135054,404341,269261) : difference with theory (-26) = 0 CORRECTING DEFECT 14 (vertices=67, convex hull=80, v0=62594) After retessellation of defect 14 (v0=62594), euler #=-25 (135078,404446,269343) : difference with theory (-25) = 0 CORRECTING DEFECT 15 (vertices=216, convex hull=137, v0=63563) After retessellation of defect 15 (v0=63563), euler #=-23 (135118,404631,269490) : difference with theory (-24) = -1 CORRECTING DEFECT 16 (vertices=9, convex hull=26, v0=63829) After retessellation of defect 16 (v0=63829), euler #=-22 (135120,404645,269503) : difference with theory (-23) = -1 CORRECTING DEFECT 17 (vertices=90, convex hull=31, v0=65502) After retessellation of defect 17 (v0=65502), euler #=-21 (135127,404675,269527) : difference with theory (-22) = -1 CORRECTING DEFECT 18 (vertices=76, convex hull=41, v0=67111) After retessellation of defect 18 (v0=67111), euler #=-20 (135142,404736,269574) : difference with theory (-21) = -1 CORRECTING DEFECT 19 (vertices=442, convex hull=378, v0=71122) normal vector of length zero at vertex 136208 with 3 faces After retessellation of defect 19 (v0=71122), euler #=-21 (135389,405678,270268) : difference with theory (-20) = 1 CORRECTING DEFECT 20 (vertices=83, convex hull=49, v0=73053) After retessellation of defect 20 (v0=73053), euler #=-20 (135399,405728,270309) : difference with theory (-19) = 1 CORRECTING DEFECT 21 (vertices=294, convex hull=56, v0=76580) After retessellation of defect 21 (v0=76580), euler #=-19 (135413,405800,270368) : difference with theory (-18) = 1 CORRECTING DEFECT 22 (vertices=22, convex hull=42, v0=81964) After retessellation of defect 22 (v0=81964), euler #=-18 (135421,405841,270402) : difference with theory (-17) = 1 CORRECTING DEFECT 23 (vertices=74, convex hull=42, v0=96175) After retessellation of defect 23 (v0=96175), euler #=-17 (135431,405886,270438) : difference with theory (-16) = 1 CORRECTING DEFECT 24 (vertices=11, convex hull=15, v0=98733) After retessellation of defect 24 (v0=98733), euler #=-16 (135434,405898,270448) : difference with theory (-15) = 1 CORRECTING DEFECT 25 (vertices=161, convex hull=142, v0=100971) After retessellation of defect 25 (v0=100971), euler #=-14 (135505,406182,270663) : difference with theory (-14) = 0 CORRECTING DEFECT 26 (vertices=7, convex hull=16, v0=102772) After retessellation of defect 26 (v0=102772), euler #=-13 (135507,406192,270672) : difference with theory (-13) = 0 CORRECTING DEFECT 27 (vertices=25, convex hull=30, v0=105680) After retessellation of defect 27 (v0=105680), euler #=-12 (135511,406217,270694) : difference with theory (-12) = 0 CORRECTING DEFECT 28 (vertices=18, convex hull=35, v0=107135) After retessellation of defect 28 (v0=107135), euler #=-11 (135512,406232,270709) : difference with theory (-11) = 0 CORRECTING DEFECT 29 (vertices=20, convex hull=31, v0=107332) After retessellation of defect 29 (v0=107332), euler #=-10 (135515,406250,270725) : difference with theory (-10) = 0 CORRECTING DEFECT 30 (vertices=8, convex hull=27, v0=109431) After retessellation of defect 30 (v0=109431), euler #=-9 (135516,406257,270732) : difference with theory (-9) = 0 CORRECTING DEFECT 31 (vertices=33, convex hull=62, v0=110023) After retessellation of defect 31 (v0=110023), euler #=-8 (135536,406341,270797) : difference with theory (-8) = 0 CORRECTING DEFECT 32 (vertices=20, convex hull=44, v0=113347) After retessellation of defect 32 (v0=113347), euler #=-7 (135545,406382,270830) : difference with theory (-7) = 0 CORRECTING DEFECT 33 (vertices=37, convex hull=72, v0=116330) After retessellation of defect 33 (v0=116330), euler #=-6 (135561,406456,270889) : difference with theory (-6) = 0 CORRECTING DEFECT 34 (vertices=35, convex hull=75, v0=118166) After retessellation of defect 34 (v0=118166), euler #=-5 (135576,406532,270951) : difference with theory (-5) = 0 CORRECTING DEFECT 35 (vertices=25, convex hull=58, v0=132499) After retessellation of defect 35 (v0=132499), euler #=-4 (135585,406582,270993) : difference with theory (-4) = 0 CORRECTING DEFECT 36 (vertices=27, convex hull=68, v0=132886) After retessellation of defect 36 (v0=132886), euler #=-3 (135602,406662,271057) : difference with theory (-3) = 0 CORRECTING DEFECT 37 (vertices=42, convex hull=63, v0=133364) After retessellation of defect 37 (v0=133364), euler #=-2 (135623,406750,271125) : difference with theory (-2) = 0 CORRECTING DEFECT 38 (vertices=34, convex hull=60, v0=134390) After retessellation of defect 38 (v0=134390), euler #=-1 (135640,406825,271184) : difference with theory (-1) = 0 CORRECTING DEFECT 39 (vertices=129, convex hull=67, v0=134779) After retessellation of defect 39 (v0=134779), euler #=0 (135663,406923,271260) : difference with theory (0) = 0 CORRECTING DEFECT 40 (vertices=29, convex hull=63, v0=134947) After retessellation of defect 40 (v0=134947), euler #=1 (135677,406990,271314) : difference with theory (1) = 0 CORRECTING DEFECT 41 (vertices=37, convex hull=84, v0=135957) After retessellation of defect 41 (v0=135957), euler #=2 (135698,407088,271392) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->13.44) (max @ vno 55647 --> 60516) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->13.44) (max @ vno 55647 --> 60516) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 125 mutations (36.1%), 221 crossovers (63.9%), 64 vertices were eliminated building final representation... 1940 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=135698, nf=271392, ne=407088, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 19.5 minutes 0 defective edges removing intersecting faces 000: 265 intersecting 001: 12 intersecting mris_fix_topology utimesec 1171.905843 mris_fix_topology stimesec 0.394939 mris_fix_topology ru_maxrss 429948 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 54861 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 12992 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 365 mris_fix_topology ru_nivcsw 4020 FSRUNTIME@ mris_fix_topology rh 0.3256 hours 1 threads PIDs (6397 6400) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 136564 - 409686 + 273124 = 2 --> 0 holes F =2V-4: 273124 = 273128-4 (0) 2E=3F: 819372 = 819372 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 135698 - 407088 + 271392 = 2 --> 0 holes F =2V-4: 271392 = 271396-4 (0) 2E=3F: 814176 = 814176 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 48 intersecting 001: 14 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 50 intersecting 001: 8 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Oct 7 22:13:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 lh #-------------------------------------------- #@# Make White Surf rh Sat Oct 7 22:13:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 rh Waiting for PID 7870 of (7870 7873) to complete... Waiting for PID 7873 of (7870 7873) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... 23920 bright wm thresholded. 3496 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.orig... computing class statistics... border white: 249299 voxels (1.49%) border gray 297398 voxels (1.77%) WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0] GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.5 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 39.9 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 29.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->3.63) (max @ vno 115332 --> 116189) face area 0.27 +- 0.12 (0.00-->3.18) mean absolute distance = 0.63 +- 0.74 4116 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=61+-7.8 mean inside = 91.7, mean outside = 70.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=75.7, 59 (59) missing vertices, mean dist 0.3 [0.5 (%36.0)->0.7 (%64.0))] %78 local maxima, %18 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 0.92 +- 0.25 (0.11-->3.82) (max @ vno 115332 --> 116189) face area 0.27 +- 0.13 (0.00-->2.66) mean absolute distance = 0.31 +- 0.49 3020 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4118089.0, rms=11.674 001: dt: 0.5000, sse=2274381.8, rms=8.173 (29.989%) 002: dt: 0.5000, sse=1532191.5, rms=6.204 (24.088%) 003: dt: 0.5000, sse=1199868.9, rms=5.090 (17.965%) 004: dt: 0.5000, sse=1048864.0, rms=4.467 (12.230%) 005: dt: 0.5000, sse=982180.4, rms=4.182 (6.381%) 006: dt: 0.5000, sse=957553.6, rms=4.049 (3.187%) 007: dt: 0.5000, sse=944733.2, rms=3.994 (1.357%) rms = 3.95, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=934191.0, rms=3.948 (1.153%) 009: dt: 0.2500, sse=712399.4, rms=2.565 (35.019%) 010: dt: 0.2500, sse=663023.4, rms=2.151 (16.164%) 011: dt: 0.2500, sse=651300.8, rms=2.038 (5.248%) 012: dt: 0.2500, sse=645632.5, rms=1.983 (2.671%) rms = 1.94, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=641662.8, rms=1.942 (2.066%) 014: dt: 0.1250, sse=630543.9, rms=1.827 (5.924%) rms = 1.81, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=629182.4, rms=1.810 (0.945%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.0, 65 (19) missing vertices, mean dist -0.2 [0.3 (%73.0)->0.2 (%27.0))] %83 local maxima, %12 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 0.90 +- 0.25 (0.12-->4.18) (max @ vno 108799 --> 107907) face area 0.35 +- 0.16 (0.00-->3.37) mean absolute distance = 0.23 +- 0.36 2932 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1344469.5, rms=5.022 016: dt: 0.5000, sse=982940.6, rms=3.372 (32.846%) rms = 3.75, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=839373.9, rms=2.423 (28.159%) 018: dt: 0.2500, sse=782857.2, rms=1.909 (21.212%) 019: dt: 0.2500, sse=763263.6, rms=1.695 (11.192%) 020: dt: 0.2500, sse=756913.1, rms=1.621 (4.346%) rms = 1.58, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=752598.4, rms=1.579 (2.613%) 022: dt: 0.1250, sse=745808.8, rms=1.477 (6.467%) rms = 1.46, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=743511.8, rms=1.462 (1.037%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.2, 54 (9) missing vertices, mean dist -0.1 [0.3 (%67.1)->0.2 (%32.9))] %87 local maxima, % 8 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 0.90 +- 0.25 (0.05-->4.39) (max @ vno 108799 --> 107907) face area 0.34 +- 0.16 (0.00-->3.31) mean absolute distance = 0.22 +- 0.32 2816 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=929087.4, rms=3.169 rms = 3.15, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=931729.7, rms=3.153 (0.486%) 025: dt: 0.2500, sse=757017.4, rms=1.841 (41.627%) 026: dt: 0.2500, sse=727541.6, rms=1.509 (18.027%) rms = 1.48, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=724687.8, rms=1.484 (1.642%) 028: dt: 0.1250, sse=711280.2, rms=1.295 (12.726%) rms = 1.28, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=710446.1, rms=1.279 (1.282%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.0, 60 (4) missing vertices, mean dist -0.0 [0.2 (%55.7)->0.2 (%44.3))] %89 local maxima, % 6 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-6.0.0/0051105/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=732282.2, rms=1.693 rms = 2.17, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=696679.4, rms=1.158 (31.581%) 031: dt: 0.2500, sse=682944.9, rms=0.958 (17.302%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=681152.0, rms=0.952 (0.577%) positioning took 0.4 minutes generating cortex label... 6 non-cortical segments detected only using segment with 7076 vertices erasing segment 1 (vno[0] = 67299) erasing segment 2 (vno[0] = 100962) erasing segment 3 (vno[0] = 101069) erasing segment 4 (vno[0] = 105965) erasing segment 5 (vno[0] = 109610) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.area vertex spacing 0.89 +- 0.25 (0.01-->4.41) (max @ vno 107907 --> 108799) face area 0.33 +- 0.16 (0.00-->3.32) refinement took 5.3 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... 23920 bright wm thresholded. 3496 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.orig... computing class statistics... border white: 249299 voxels (1.49%) border gray 297398 voxels (1.77%) WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0] GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.5 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 40.9 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->5.42) (max @ vno 55647 --> 60516) face area 0.27 +- 0.12 (0.00-->3.93) mean absolute distance = 0.64 +- 0.75 4054 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.0, GM=62+-7.8 mean inside = 91.5, mean outside = 70.4 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=76.0, 53 (53) missing vertices, mean dist 0.3 [0.5 (%37.7)->0.7 (%62.3))] %75 local maxima, %20 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 0.92 +- 0.25 (0.13-->5.06) (max @ vno 55647 --> 60516) face area 0.27 +- 0.13 (0.00-->2.90) mean absolute distance = 0.31 +- 0.50 3082 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3969590.0, rms=11.490 001: dt: 0.5000, sse=2178555.5, rms=7.990 (30.465%) 002: dt: 0.5000, sse=1466748.1, rms=6.039 (24.412%) 003: dt: 0.5000, sse=1145249.5, rms=4.919 (18.547%) 004: dt: 0.5000, sse=1007150.8, rms=4.340 (11.769%) 005: dt: 0.5000, sse=963890.9, rms=4.070 (6.228%) 006: dt: 0.5000, sse=925727.3, rms=3.957 (2.783%) 007: dt: 0.5000, sse=916690.8, rms=3.903 (1.350%) rms = 3.88, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=911521.9, rms=3.876 (0.692%) 009: dt: 0.2500, sse=692211.3, rms=2.473 (36.206%) 010: dt: 0.2500, sse=645961.0, rms=2.062 (16.622%) 011: dt: 0.2500, sse=635521.1, rms=1.961 (4.879%) 012: dt: 0.2500, sse=630563.8, rms=1.886 (3.837%) rms = 1.86, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=626312.6, rms=1.859 (1.415%) 014: dt: 0.1250, sse=615245.8, rms=1.721 (7.419%) rms = 1.71, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=612738.2, rms=1.706 (0.890%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=79.2, 58 (17) missing vertices, mean dist -0.2 [0.3 (%72.0)->0.2 (%28.0))] %81 local maxima, %14 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 0.90 +- 0.25 (0.08-->4.90) (max @ vno 55647 --> 60516) face area 0.35 +- 0.16 (0.00-->3.31) mean absolute distance = 0.23 +- 0.37 2824 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1295973.8, rms=4.877 016: dt: 0.5000, sse=975937.0, rms=3.371 (30.892%) rms = 3.73, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=833973.0, rms=2.433 (27.827%) 018: dt: 0.2500, sse=778558.4, rms=1.935 (20.477%) 019: dt: 0.2500, sse=757235.8, rms=1.711 (11.535%) 020: dt: 0.2500, sse=750094.4, rms=1.636 (4.429%) 021: dt: 0.2500, sse=745283.4, rms=1.568 (4.121%) rms = 1.54, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=742279.2, rms=1.538 (1.928%) 023: dt: 0.1250, sse=734379.1, rms=1.440 (6.389%) rms = 1.43, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=733666.0, rms=1.429 (0.756%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 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 3 vertex label from ripped group mean border=81.3, 47 (9) missing vertices, mean dist -0.1 [0.3 (%66.1)->0.2 (%33.9))] %86 local maxima, % 9 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 0.90 +- 0.25 (0.04-->4.84) (max @ vno 55647 --> 60516) face area 0.34 +- 0.16 (0.00-->3.01) mean absolute distance = 0.22 +- 0.32 2663 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=894831.4, rms=3.003 rms = 3.09, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=778272.4, rms=2.109 (29.765%) 026: dt: 0.2500, sse=721058.1, rms=1.454 (31.080%) 027: dt: 0.2500, sse=711154.8, rms=1.358 (6.550%) rms = 1.33, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=710539.4, rms=1.332 (1.929%) 029: dt: 0.1250, sse=704820.5, rms=1.253 (5.937%) rms = 1.25, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=703658.8, rms=1.254 (-0.039%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.0, 55 (9) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %88 local maxima, % 7 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-6.0.0/0051105/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=726628.0, rms=1.662 rms = 2.14, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=687874.9, rms=1.142 (31.298%) 032: dt: 0.2500, sse=677089.9, rms=0.939 (17.752%) rms = 0.95, time step reduction 2 of 3 to 0.125... rms = 0.93, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=676474.2, rms=0.933 (0.677%) positioning took 0.4 minutes generating cortex label... 17 non-cortical segments detected only using segment with 7102 vertices erasing segment 0 (vno[0] = 48875) erasing segment 1 (vno[0] = 48924) erasing segment 3 (vno[0] = 66100) erasing segment 4 (vno[0] = 72686) erasing segment 5 (vno[0] = 74955) erasing segment 6 (vno[0] = 77311) erasing segment 7 (vno[0] = 79385) erasing segment 8 (vno[0] = 79404) erasing segment 9 (vno[0] = 81512) erasing segment 10 (vno[0] = 96586) erasing segment 11 (vno[0] = 100480) erasing segment 12 (vno[0] = 101352) erasing segment 13 (vno[0] = 103130) erasing segment 14 (vno[0] = 104099) erasing segment 15 (vno[0] = 108701) erasing segment 16 (vno[0] = 119686) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.area vertex spacing 0.89 +- 0.25 (0.01-->4.82) (max @ vno 55647 --> 60516) face area 0.33 +- 0.16 (0.00-->3.00) refinement took 5.5 minutes PIDs (7870 7873) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sat Oct 7 22:18:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Oct 7 22:18:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 8056 of (8056 8059) to complete... Waiting for PID 8059 of (8056 8059) 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 (8056 8059) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Oct 7 22:18:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Oct 7 22:18:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 8101 of (8101 8104) to complete... Waiting for PID 8104 of (8101 8104) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.5 mm, total surface area = 82185 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.182 (target=0.015) step 005: RMS=0.128 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 44.504234 mris_inflate stimesec 0.111982 mris_inflate ru_maxrss 200012 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29117 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10696 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2236 mris_inflate ru_nivcsw 3389 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.3 mm, total surface area = 81800 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.184 (target=0.015) step 005: RMS=0.128 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 44.185282 mris_inflate stimesec 0.106983 mris_inflate ru_maxrss 198608 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28765 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10632 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2175 mris_inflate ru_nivcsw 3378 PIDs (8101 8104) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Oct 7 22:19:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 Sat Oct 7 22:19:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 8201 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8204 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8207 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8210 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8213 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8216 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8219 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8222 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8225 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8229 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8232 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... Waiting for PID 8235 of (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 9.810*4pi (123.271) --> -9 handles ICI = 190.1, FI = 1871.4, variation=29721.109 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 167 vertices thresholded to be in k1 ~ [-0.38 0.73], k2 ~ [-0.22 0.14] total integrated curvature = 0.594*4pi (7.462) --> 0 handles ICI = 1.5, FI = 7.5, variation=138.071 122 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 72 vertices thresholded to be in [-0.12 0.16] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.020 done. mris_curvature -w rh.white.preaparc total integrated curvature = 2.007*4pi (25.216) --> -1 handles ICI = 185.7, FI = 1854.1, variation=29716.497 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 162 vertices thresholded to be in k1 ~ [-0.21 0.71], k2 ~ [-0.30 0.09] total integrated curvature = 0.520*4pi (6.535) --> 0 handles ICI = 1.5, FI = 8.5, variation=149.025 158 vertices thresholded to be in [-0.10 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 96 vertices thresholded to be in [-0.12 0.21] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022 done. PIDs (8201 8204 8207 8210 8213 8216 8219 8222 8225 8229 8232 8235) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sat Oct 7 22:20:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051105 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 [ 0051105/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 [ 267 ] Gb_filter = 0 WARN: S lookup min: -1.542588 WARN: S explicit min: 0.000000 vertex = 1229 #----------------------------------------- #@# Curvature Stats rh Sat Oct 7 22:21:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051105 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 [ 0051105/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 [ 250 ] Gb_filter = 0 WARN: S lookup min: -0.239601 WARN: S explicit min: 0.000000 vertex = 1528 #-------------------------------------------- #@# Sphere lh Sat Oct 7 22:21:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Oct 7 22:21:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 8390 of (8390 8393) to complete... Waiting for PID 8393 of (8390 8393) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 2 == scaling brain by 0.312... 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 %20.23 pass 1: epoch 2 of 3 starting distance error %20.21 unfolding complete - removing small folds... starting distance error %20.08 removing remaining folds... final distance error %20.11 MRISunfold() return, current seed 1234 -01: dt=0.0000, 211 negative triangles 198: dt=0.9900, 211 negative triangles 199: dt=0.9900, 103 negative triangles 200: dt=0.9900, 80 negative triangles 201: dt=0.9900, 68 negative triangles 202: dt=0.9900, 69 negative triangles 203: dt=0.9900, 61 negative triangles 204: dt=0.9900, 62 negative triangles 205: dt=0.9900, 58 negative triangles 206: dt=0.9900, 53 negative triangles 207: dt=0.9900, 48 negative triangles 208: dt=0.9900, 44 negative triangles 209: dt=0.9900, 46 negative triangles 210: dt=0.9900, 41 negative triangles 211: dt=0.9900, 44 negative triangles 212: dt=0.9900, 42 negative triangles 213: dt=0.9900, 47 negative triangles 214: dt=0.9900, 36 negative triangles 215: dt=0.9900, 35 negative triangles 216: dt=0.9900, 38 negative triangles 217: dt=0.9900, 39 negative triangles 218: dt=0.9900, 36 negative triangles 219: dt=0.9900, 36 negative triangles 220: dt=0.9900, 34 negative triangles 221: dt=0.9900, 35 negative triangles 222: dt=0.9900, 34 negative triangles 223: dt=0.9900, 28 negative triangles 224: dt=0.9900, 29 negative triangles 225: dt=0.9900, 32 negative triangles 226: dt=0.9900, 28 negative triangles 227: dt=0.9900, 22 negative triangles 228: dt=0.9900, 22 negative triangles 229: dt=0.9900, 28 negative triangles 230: dt=0.9900, 22 negative triangles 231: dt=0.9900, 14 negative triangles 232: dt=0.9900, 16 negative triangles 233: dt=0.9900, 21 negative triangles 234: dt=0.9900, 17 negative triangles 235: dt=0.9900, 15 negative triangles 236: dt=0.9900, 15 negative triangles 237: dt=0.9900, 15 negative triangles 238: dt=0.9900, 15 negative triangles 239: dt=0.9900, 12 negative triangles 240: dt=0.9900, 10 negative triangles 241: dt=0.9900, 12 negative triangles 242: dt=0.9900, 13 negative triangles 243: dt=0.9900, 9 negative triangles 244: dt=0.9900, 6 negative triangles 245: dt=0.9900, 9 negative triangles 246: dt=0.9900, 8 negative triangles 247: dt=0.9900, 10 negative triangles 248: dt=0.9900, 9 negative triangles 249: dt=0.9900, 6 negative triangles 250: dt=0.9900, 8 negative triangles 251: dt=0.9900, 7 negative triangles 252: dt=0.9900, 8 negative triangles 253: dt=0.9900, 10 negative triangles 254: dt=0.9405, 8 negative triangles 255: dt=0.9405, 6 negative triangles 256: dt=0.9405, 8 negative triangles 257: dt=0.9405, 6 negative triangles 258: dt=0.9405, 8 negative triangles 259: dt=0.9405, 10 negative triangles 260: dt=0.9405, 8 negative triangles 261: dt=0.9405, 6 negative triangles 262: dt=0.9405, 8 negative triangles 263: dt=0.9405, 6 negative triangles 264: dt=0.8935, 8 negative triangles 265: dt=0.8935, 10 negative triangles 266: dt=0.8935, 8 negative triangles 267: dt=0.8935, 5 negative triangles 268: dt=0.8935, 7 negative triangles 269: dt=0.8935, 4 negative triangles 270: dt=0.8935, 6 negative triangles 271: dt=0.8935, 4 negative triangles 272: dt=0.8935, 6 negative triangles 273: dt=0.8935, 5 negative triangles 274: dt=0.8935, 7 negative triangles 275: dt=0.8935, 5 negative triangles 276: dt=0.8935, 1 negative triangles 277: dt=0.8935, 1 negative triangles 278: dt=0.8935, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.03 hours mris_sphere utimesec 3716.487008 mris_sphere stimesec 2.055687 mris_sphere ru_maxrss 281280 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49580 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9688 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 146436 mris_sphere ru_nivcsw 315771 FSRUNTIME@ mris_sphere 1.0320 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 2 == scaling brain by 0.316... 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 %20.21 pass 1: epoch 2 of 3 starting distance error %20.18 unfolding complete - removing small folds... starting distance error %20.09 removing remaining folds... final distance error %20.11 MRISunfold() return, current seed 1234 -01: dt=0.0000, 179 negative triangles 212: dt=0.9900, 179 negative triangles 213: dt=0.9900, 84 negative triangles 214: dt=0.9900, 59 negative triangles 215: dt=0.9900, 49 negative triangles 216: dt=0.9900, 32 negative triangles 217: dt=0.9900, 33 negative triangles 218: dt=0.9900, 29 negative triangles 219: dt=0.9900, 17 negative triangles 220: dt=0.9900, 14 negative triangles 221: dt=0.9900, 11 negative triangles 222: dt=0.9900, 12 negative triangles 223: dt=0.9900, 11 negative triangles 224: dt=0.9900, 7 negative triangles 225: dt=0.9900, 3 negative triangles 226: dt=0.9900, 11 negative triangles 227: dt=0.9900, 5 negative triangles 228: dt=0.9900, 3 negative triangles 229: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.05 hours mris_sphere utimesec 3806.646301 mris_sphere stimesec 1.799726 mris_sphere ru_maxrss 279364 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49089 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9576 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 154467 mris_sphere ru_nivcsw 312096 FSRUNTIME@ mris_sphere 1.0470 hours 1 threads PIDs (8390 8393) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Oct 7 23:23:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 Sat Oct 7 23:23:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 10683 of (10683 10686) to complete... Waiting for PID 10686 of (10683 10686) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 5.622 curvature mean = 0.026, std = 0.813 curvature mean = 0.018, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, -8.00) sse = 257169.6, tmin=2.1614 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 237371.9, tmin=3.3282 d=8.00 min @ (0.00, 2.00, 2.00) sse = 228214.8, tmin=4.5179 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 226869.7, tmin=5.7004 d=2.00 min @ (0.50, 0.50, -0.50) sse = 226211.0, tmin=6.8737 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 226111.8, tmin=8.0357 d=0.50 min @ (0.00, -0.12, 0.00) sse = 226063.6, tmin=9.2013 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 9.20 min curvature mean = -0.003, std = 0.826 curvature mean = 0.005, std = 0.943 curvature mean = -0.004, std = 0.837 curvature mean = 0.002, std = 0.977 curvature mean = -0.005, std = 0.840 curvature mean = 0.000, std = 0.991 2 Reading smoothwm curvature mean = -0.031, std = 0.682 curvature mean = 0.040, std = 0.248 curvature mean = 0.031, std = 0.151 curvature mean = 0.035, std = 0.307 curvature mean = 0.020, std = 0.236 curvature mean = 0.034, std = 0.333 curvature mean = 0.012, std = 0.306 curvature mean = 0.034, std = 0.345 curvature mean = 0.004, std = 0.381 MRISregister() return, current seed 0 -01: dt=0.0000, 81 negative triangles 115: dt=0.9900, 81 negative triangles expanding nbhd size to 1 116: dt=0.9900, 102 negative triangles 117: dt=0.9900, 76 negative triangles 118: dt=0.9900, 76 negative triangles 119: dt=0.9900, 84 negative triangles 120: dt=0.9900, 84 negative triangles 121: dt=0.9900, 82 negative triangles 122: dt=0.9900, 86 negative triangles 123: dt=0.9900, 78 negative triangles 124: dt=0.9900, 85 negative triangles 125: dt=0.9900, 80 negative triangles 126: dt=0.9900, 75 negative triangles 127: dt=0.9900, 85 negative triangles 128: dt=0.9900, 71 negative triangles 129: dt=0.9900, 75 negative triangles 130: dt=0.9900, 70 negative triangles 131: dt=0.9900, 71 negative triangles 132: dt=0.9900, 71 negative triangles 133: dt=0.9900, 67 negative triangles 134: dt=0.9900, 67 negative triangles 135: dt=0.9900, 67 negative triangles 136: dt=0.9900, 68 negative triangles 137: dt=0.9900, 65 negative triangles 138: dt=0.9900, 57 negative triangles 139: dt=0.9900, 54 negative triangles 140: dt=0.9900, 54 negative triangles 141: dt=0.9900, 58 negative triangles 142: dt=0.9900, 51 negative triangles 143: dt=0.9900, 47 negative triangles 144: dt=0.9900, 43 negative triangles 145: dt=0.9900, 35 negative triangles 146: dt=0.9900, 38 negative triangles 147: dt=0.9900, 29 negative triangles 148: dt=0.9900, 32 negative triangles 149: dt=0.9900, 34 negative triangles 150: dt=0.9900, 25 negative triangles 151: dt=0.9900, 26 negative triangles 152: dt=0.9900, 18 negative triangles 153: dt=0.9900, 18 negative triangles 154: dt=0.9900, 12 negative triangles 155: dt=0.9900, 9 negative triangles 156: dt=0.9900, 14 negative triangles 157: dt=0.9900, 10 negative triangles 158: dt=0.9900, 9 negative triangles 159: dt=0.9900, 8 negative triangles 160: dt=0.9900, 6 negative triangles 161: dt=0.9900, 5 negative triangles 162: dt=0.9900, 4 negative triangles 163: dt=0.9900, 5 negative triangles 164: dt=0.9900, 5 negative triangles 165: dt=0.9900, 3 negative triangles 166: dt=0.9900, 3 negative triangles 167: dt=0.9900, 2 negative triangles 168: dt=0.9900, 3 negative triangles 169: dt=0.9900, 3 negative triangles 170: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.58 hours mris_register utimesec 5675.695163 mris_register stimesec 6.955942 mris_register ru_maxrss 255116 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 35166 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 9712 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 391579 mris_register ru_nivcsw 262835 FSRUNTIME@ mris_register 1.5785 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 5.535 curvature mean = 0.032, std = 0.818 curvature mean = 0.018, std = 0.859 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 344245.8, tmin=1.0366 d=32.00 min @ (0.00, 8.00, -8.00) sse = 232640.5, tmin=2.1623 d=16.00 min @ (4.00, 0.00, 4.00) sse = 224522.1, tmin=3.3291 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 211512.3, tmin=4.5188 d=2.00 min @ (0.50, -0.50, 0.00) sse = 210704.9, tmin=6.8586 d=1.00 min @ (0.00, 0.25, 0.00) sse = 210680.2, tmin=8.0140 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 210635.5, tmin=9.1740 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 9.17 min curvature mean = 0.010, std = 0.828 curvature mean = 0.007, std = 0.945 curvature mean = 0.007, std = 0.837 curvature mean = 0.003, std = 0.978 curvature mean = 0.006, std = 0.839 curvature mean = 0.000, std = 0.991 2 Reading smoothwm curvature mean = -0.028, std = 0.317 curvature mean = 0.036, std = 0.241 curvature mean = 0.064, std = 0.324 curvature mean = 0.030, std = 0.300 curvature mean = 0.039, std = 0.502 curvature mean = 0.028, std = 0.328 curvature mean = 0.022, std = 0.640 curvature mean = 0.028, std = 0.339 curvature mean = 0.008, std = 0.753 MRISregister() return, current seed 0 -01: dt=0.0000, 100 negative triangles 113: dt=0.9900, 100 negative triangles expanding nbhd size to 1 114: dt=0.9900, 109 negative triangles 115: dt=0.9900, 99 negative triangles 116: dt=0.9900, 96 negative triangles 117: dt=0.9900, 101 negative triangles 118: dt=0.9900, 89 negative triangles 119: dt=0.9900, 92 negative triangles 120: dt=0.9900, 81 negative triangles 121: dt=0.9900, 82 negative triangles 122: dt=0.9900, 78 negative triangles 123: dt=0.9900, 76 negative triangles 124: dt=0.9900, 75 negative triangles 125: dt=0.9900, 69 negative triangles 126: dt=0.9900, 66 negative triangles 127: dt=0.9900, 66 negative triangles 128: dt=0.9900, 64 negative triangles 129: dt=0.9900, 63 negative triangles 130: dt=0.9900, 58 negative triangles 131: dt=0.9900, 55 negative triangles 132: dt=0.9900, 55 negative triangles 133: dt=0.9900, 51 negative triangles 134: dt=0.9900, 52 negative triangles 135: dt=0.9900, 47 negative triangles 136: dt=0.9900, 49 negative triangles 137: dt=0.9900, 48 negative triangles 138: dt=0.9900, 45 negative triangles 139: dt=0.9900, 47 negative triangles 140: dt=0.9900, 49 negative triangles 141: dt=0.9900, 48 negative triangles 142: dt=0.9900, 47 negative triangles 143: dt=0.9900, 45 negative triangles 144: dt=0.9900, 41 negative triangles 145: dt=0.9900, 41 negative triangles 146: dt=0.9900, 43 negative triangles 147: dt=0.9900, 39 negative triangles 148: dt=0.9900, 38 negative triangles 149: dt=0.9900, 40 negative triangles 150: dt=0.9900, 38 negative triangles 151: dt=0.9900, 37 negative triangles 152: dt=0.9900, 33 negative triangles 153: dt=0.9900, 29 negative triangles 154: dt=0.9900, 29 negative triangles 155: dt=0.9900, 32 negative triangles 156: dt=0.9900, 27 negative triangles 157: dt=0.9900, 28 negative triangles 158: dt=0.9900, 25 negative triangles 159: dt=0.9900, 25 negative triangles 160: dt=0.9900, 26 negative triangles 161: dt=0.9900, 29 negative triangles 162: dt=0.9900, 21 negative triangles 163: dt=0.9900, 22 negative triangles 164: dt=0.9900, 22 negative triangles 165: dt=0.9900, 20 negative triangles 166: dt=0.9900, 17 negative triangles 167: dt=0.9900, 17 negative triangles 168: dt=0.9900, 16 negative triangles 169: dt=0.9900, 11 negative triangles 170: dt=0.9900, 10 negative triangles 171: dt=0.9900, 10 negative triangles 172: dt=0.9900, 10 negative triangles 173: dt=0.9900, 7 negative triangles 174: dt=0.9900, 6 negative triangles 175: dt=0.9900, 5 negative triangles 176: dt=0.9900, 3 negative triangles 177: dt=0.9900, 3 negative triangles 178: dt=0.9900, 2 negative triangles 179: dt=0.9900, 2 negative triangles 180: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.58 hours mris_register utimesec 5679.435594 mris_register stimesec 5.474167 mris_register ru_maxrss 254276 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 37233 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 9552 mris_register ru_oublock 9648 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 398441 mris_register ru_nivcsw 251270 FSRUNTIME@ mris_register 1.5787 hours 1 threads PIDs (10683 10686) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 00:58:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 00:58:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 17579 of (17579 17582) to complete... Waiting for PID 17582 of (17579 17582) 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 (17579 17582) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 00:58:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 8 00:58:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 17624 of (17624 17627) to complete... Waiting for PID 17627 of (17624 17627) 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 (17624 17627) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 00:58:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 8 00:58:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 17675 of (17675 17678) to complete... Waiting for PID 17678 of (17675 17678) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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... 1176 labels changed using aseg relabeling using gibbs priors... 000: 3171 changed, 136564 examined... 001: 775 changed, 13440 examined... 002: 204 changed, 4260 examined... 003: 59 changed, 1228 examined... 004: 20 changed, 341 examined... 005: 4 changed, 113 examined... 006: 2 changed, 30 examined... 007: 2 changed, 10 examined... 008: 1 changed, 11 examined... 009: 0 changed, 7 examined... 260 labels changed using aseg 000: 125 total segments, 74 labels (318 vertices) changed 001: 52 total segments, 1 labels (1 vertices) changed 002: 51 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 16 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1341 vertices marked for relabeling... 1341 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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... 960 labels changed using aseg relabeling using gibbs priors... 000: 2740 changed, 135698 examined... 001: 634 changed, 11920 examined... 002: 179 changed, 3502 examined... 003: 51 changed, 1087 examined... 004: 18 changed, 302 examined... 005: 11 changed, 112 examined... 006: 8 changed, 61 examined... 007: 2 changed, 38 examined... 008: 1 changed, 14 examined... 009: 2 changed, 8 examined... 010: 4 changed, 11 examined... 011: 3 changed, 12 examined... 012: 1 changed, 14 examined... 013: 0 changed, 6 examined... 139 labels changed using aseg 000: 85 total segments, 42 labels (167 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1280 vertices marked for relabeling... 1280 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 14 seconds. PIDs (17675 17678) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 00:58:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 00:58:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 rh Waiting for PID 17723 of (17723 17726) to complete... Waiting for PID 17726 of (17723 17726) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... 23920 bright wm thresholded. 3496 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.orig... computing class statistics... border white: 249299 voxels (1.49%) border gray 297398 voxels (1.77%) WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0] GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.5 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 39.9 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 29.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=61+-7.8 mean inside = 91.7, mean outside = 70.4 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 0.89 +- 0.25 (0.01-->4.41) (max @ vno 107907 --> 108799) face area 0.33 +- 0.16 (0.00-->3.30) mean absolute distance = 0.53 +- 0.74 2966 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 107 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 5 with 218 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 76 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 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 5 points - only 0.00% unknown mean border=75.2, 79 (77) missing vertices, mean dist 0.3 [0.6 (%16.0)->0.5 (%84.0))] %75 local maxima, %20 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 0.92 +- 0.26 (0.10-->4.60) (max @ vno 108799 --> 107907) face area 0.33 +- 0.16 (0.00-->3.12) mean absolute distance = 0.32 +- 0.51 3177 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2700460.2, rms=8.853 001: dt: 0.5000, sse=1383195.8, rms=5.277 (40.391%) 002: dt: 0.5000, sse=1086298.4, rms=4.101 (22.291%) 003: dt: 0.5000, sse=1048583.6, rms=3.925 (4.294%) 004: dt: 0.5000, sse=1007907.1, rms=3.727 (5.025%) rms = 3.83, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=830177.3, rms=2.612 (29.936%) 006: dt: 0.2500, sse=781010.3, rms=2.108 (19.300%) 007: dt: 0.2500, sse=753680.6, rms=1.926 (8.611%) 008: dt: 0.2500, sse=747226.1, rms=1.869 (2.979%) rms = 1.82, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=743816.6, rms=1.820 (2.618%) 010: dt: 0.1250, sse=735167.1, rms=1.732 (4.848%) rms = 1.72, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=734046.4, rms=1.717 (0.816%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 92 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 155 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 16 with 4 points - only 0.00% unknown mean border=78.8, 81 (17) missing vertices, mean dist -0.2 [0.4 (%74.1)->0.2 (%25.9))] %83 local maxima, %13 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 0.91 +- 0.25 (0.06-->4.26) (max @ vno 108799 --> 107907) face area 0.36 +- 0.17 (0.00-->3.53) mean absolute distance = 0.24 +- 0.38 3074 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1371763.1, rms=5.061 012: dt: 0.5000, sse=1001176.1, rms=3.325 (34.312%) rms = 3.65, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=852238.9, rms=2.371 (28.688%) 014: dt: 0.2500, sse=790474.9, rms=1.819 (23.255%) 015: dt: 0.2500, sse=770429.6, rms=1.585 (12.884%) 016: dt: 0.2500, sse=766275.6, rms=1.518 (4.204%) rms = 1.49, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=762311.8, rms=1.486 (2.116%) 018: dt: 0.1250, sse=758721.0, rms=1.379 (7.231%) rms = 1.39, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=754637.3, rms=1.389 (-0.705%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 100 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 167 points - only 0.00% unknown deleting segment 5 with 7 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 9 points - only 0.00% unknown deleting segment 8 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown mean border=81.1, 69 (8) missing vertices, mean dist -0.1 [0.3 (%67.5)->0.2 (%32.5))] %87 local maxima, % 8 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 0.90 +- 0.25 (0.07-->4.15) (max @ vno 108804 --> 107913) face area 0.34 +- 0.17 (0.00-->3.38) mean absolute distance = 0.22 +- 0.32 2814 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=945537.9, rms=3.178 rms = 3.15, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=944300.2, rms=3.146 (1.006%) 021: dt: 0.2500, sse=763459.4, rms=1.803 (42.701%) 022: dt: 0.2500, sse=739061.2, rms=1.467 (18.634%) rms = 1.46, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=741841.8, rms=1.457 (0.657%) 024: dt: 0.1250, sse=719198.1, rms=1.259 (13.611%) rms = 1.24, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=717631.1, rms=1.239 (1.612%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 108 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 146 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 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 74 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown mean border=82.0, 75 (4) missing vertices, mean dist -0.0 [0.2 (%56.1)->0.2 (%43.9))] %89 local maxima, % 6 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-6.0.0/0051105/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=739799.3, rms=1.684 rms = 2.17, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=699913.6, rms=1.133 (32.743%) 027: dt: 0.2500, sse=691625.2, rms=0.927 (18.129%) rms = 0.94, time step reduction 2 of 3 to 0.125... rms = 0.92, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=688307.7, rms=0.923 (0.490%) positioning took 0.4 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7082 vertices erasing segment 1 (vno[0] = 67299) erasing segment 2 (vno[0] = 86396) erasing segment 3 (vno[0] = 100962) erasing segment 4 (vno[0] = 105965) erasing segment 5 (vno[0] = 109610) erasing segment 6 (vno[0] = 115208) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.area vertex spacing 0.89 +- 0.26 (0.01-->4.19) (max @ vno 107907 --> 108799) face area 0.34 +- 0.16 (0.00-->3.32) 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... removing 3 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=49.4, 78 (78) missing vertices, mean dist 1.5 [1.0 (%0.0)->2.9 (%100.0))] %10 local maxima, %38 large gradients and %48 min vals, 290 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=29457250.0, rms=33.199 001: dt: 0.0500, sse=25732182.0, rms=30.978 (6.691%) 002: dt: 0.0500, sse=23073256.0, rms=29.289 (5.451%) 003: dt: 0.0500, sse=21049010.0, rms=27.935 (4.623%) 004: dt: 0.0500, sse=19425520.0, rms=26.799 (4.065%) 005: dt: 0.0500, sse=18070298.0, rms=25.813 (3.680%) 006: dt: 0.0500, sse=16907554.0, rms=24.936 (3.399%) 007: dt: 0.0500, sse=15887370.0, rms=24.140 (3.192%) 008: dt: 0.0500, sse=14979127.0, rms=23.408 (3.030%) 009: dt: 0.0500, sse=14161459.0, rms=22.730 (2.900%) 010: dt: 0.0500, sse=13418458.0, rms=22.095 (2.794%) positioning took 0.9 minutes mean border=49.1, 72 (37) missing vertices, mean dist 1.2 [0.3 (%0.0)->2.4 (%100.0))] %11 local maxima, %38 large gradients and %47 min vals, 282 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=14182640.0, rms=22.749 011: dt: 0.0500, sse=13496971.0, rms=22.164 (2.570%) 012: dt: 0.0500, sse=12866909.0, rms=21.613 (2.487%) 013: dt: 0.0500, sse=12285422.0, rms=21.091 (2.414%) 014: dt: 0.0500, sse=11747881.0, rms=20.597 (2.342%) 015: dt: 0.0500, sse=11249788.0, rms=20.128 (2.275%) 016: dt: 0.0500, sse=10787875.0, rms=19.684 (2.209%) 017: dt: 0.0500, sse=10358975.0, rms=19.261 (2.145%) 018: dt: 0.0500, sse=9960533.0, rms=18.861 (2.081%) 019: dt: 0.0500, sse=9589504.0, rms=18.480 (2.021%) 020: dt: 0.0500, sse=9244067.0, rms=18.117 (1.960%) positioning took 0.9 minutes mean border=49.1, 92 (25) missing vertices, mean dist 1.1 [0.1 (%0.6)->2.1 (%99.4))] %12 local maxima, %38 large gradients and %46 min vals, 286 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=9304085.0, rms=18.187 021: dt: 0.0500, sse=8977817.0, rms=17.840 (1.911%) 022: dt: 0.0500, sse=8673485.0, rms=17.509 (1.852%) 023: dt: 0.0500, sse=8388229.0, rms=17.194 (1.802%) 024: dt: 0.0500, sse=8122213.5, rms=16.894 (1.743%) 025: dt: 0.0500, sse=7873471.5, rms=16.609 (1.688%) 026: dt: 0.0500, sse=7640297.5, rms=16.337 (1.638%) 027: dt: 0.0500, sse=7420511.5, rms=16.076 (1.596%) 028: dt: 0.0500, sse=7211945.5, rms=15.825 (1.564%) 029: dt: 0.0500, sse=7013544.5, rms=15.581 (1.536%) 030: dt: 0.0500, sse=6824939.5, rms=15.347 (1.506%) positioning took 0.9 minutes mean border=49.0, 119 (21) missing vertices, mean dist 0.9 [0.1 (%5.7)->1.9 (%94.3))] %12 local maxima, %38 large gradients and %46 min vals, 240 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=6900011.5, rms=15.441 031: dt: 0.5000, sse=5562625.5, rms=13.674 (11.445%) 032: dt: 0.5000, sse=4612672.5, rms=12.258 (10.355%) 033: dt: 0.5000, sse=3869610.8, rms=11.025 (10.058%) 034: dt: 0.5000, sse=3272932.0, rms=9.920 (10.027%) 035: dt: 0.5000, sse=2796849.5, rms=8.942 (9.852%) 036: dt: 0.5000, sse=2412269.5, rms=8.066 (9.805%) 037: dt: 0.5000, sse=2117754.0, rms=7.325 (9.178%) 038: dt: 0.5000, sse=1902859.5, rms=6.733 (8.086%) 039: dt: 0.5000, sse=1757109.5, rms=6.300 (6.428%) 040: dt: 0.5000, sse=1655969.1, rms=5.981 (5.074%) 041: dt: 0.5000, sse=1586954.0, rms=5.753 (3.805%) 042: dt: 0.5000, sse=1541940.9, rms=5.596 (2.733%) 043: dt: 0.5000, sse=1511292.1, rms=5.490 (1.894%) 044: dt: 0.5000, sse=1493130.4, rms=5.422 (1.230%) rms = 5.37, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1479781.1, rms=5.375 (0.878%) 046: dt: 0.2500, sse=1399895.0, rms=5.034 (6.335%) 047: dt: 0.2500, sse=1374823.1, rms=4.937 (1.940%) rms = 4.94, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1375597.5, rms=4.935 (0.030%) 049: dt: 0.1250, sse=1362483.8, rms=4.878 (1.153%) rms = 4.87, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1360345.1, rms=4.869 (0.189%) positioning took 2.6 minutes mean border=48.4, 3092 (6) missing vertices, mean dist 0.1 [0.2 (%49.6)->0.6 (%50.4))] %19 local maxima, %32 large gradients and %42 min vals, 155 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=1535858.6, rms=4.783 051: dt: 0.5000, sse=1479482.8, rms=4.565 (4.568%) rms = 4.55, time step reduction 1 of 3 to 0.250... 052: dt: 0.5000, sse=1467996.2, rms=4.551 (0.312%) 053: dt: 0.2500, sse=1384189.5, rms=4.116 (9.549%) 054: dt: 0.2500, sse=1362109.9, rms=4.012 (2.532%) rms = 4.01, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1361182.6, rms=4.005 (0.167%) 056: dt: 0.1250, sse=1345501.2, rms=3.921 (2.104%) rms = 3.91, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1342467.1, rms=3.907 (0.363%) positioning took 1.2 minutes mean border=47.9, 3479 (2) missing vertices, mean dist 0.1 [0.2 (%51.8)->0.5 (%48.2))] %29 local maxima, %24 large gradients and %41 min vals, 160 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=1375968.9, rms=4.047 rms = 4.29, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1357135.5, rms=3.951 (2.356%) rms = 3.95, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1355118.9, rms=3.947 (0.114%) rms = 3.91, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1347846.5, rms=3.907 (1.009%) positioning took 0.6 minutes mean border=47.4, 6549 (2) missing vertices, mean dist 0.1 [0.2 (%50.3)->0.4 (%49.7))] %33 local maxima, %19 large gradients and %39 min vals, 172 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-6.0.0/0051105/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1369792.0, rms=4.012 rms = 4.09, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1348569.9, rms=3.909 (2.571%) 062: dt: 0.2500, sse=1324266.9, rms=3.806 (2.622%) 063: dt: 0.2500, sse=1311486.8, rms=3.750 (1.477%) 064: dt: 0.2500, sse=1295362.9, rms=3.679 (1.890%) rms = 3.65, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1288992.9, rms=3.651 (0.749%) 066: dt: 0.1250, sse=1272366.6, rms=3.557 (2.579%) rms = 3.53, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1267563.1, rms=3.534 (0.653%) positioning took 1.4 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.area.pial vertex spacing 1.03 +- 0.45 (0.03-->7.85) (max @ vno 96965 --> 95990) face area 0.41 +- 0.33 (0.00-->8.74) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136564 vertices processed 25000 of 136564 vertices processed 50000 of 136564 vertices processed 75000 of 136564 vertices processed 100000 of 136564 vertices processed 125000 of 136564 vertices processed 0 of 136564 vertices processed 25000 of 136564 vertices processed 50000 of 136564 vertices processed 75000 of 136564 vertices processed 100000 of 136564 vertices processed 125000 of 136564 vertices processed thickness calculation complete, 353:957 truncations. 27258 vertices at 0 distance 91515 vertices at 1 distance 85707 vertices at 2 distance 38117 vertices at 3 distance 12634 vertices at 4 distance 3944 vertices at 5 distance 1199 vertices at 6 distance 412 vertices at 7 distance 191 vertices at 8 distance 96 vertices at 9 distance 65 vertices at 10 distance 65 vertices at 11 distance 56 vertices at 12 distance 47 vertices at 13 distance 37 vertices at 14 distance 15 vertices at 15 distance 25 vertices at 16 distance 15 vertices at 17 distance 17 vertices at 18 distance 17 vertices at 19 distance 16 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.thickness positioning took 15.6 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051105 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-6.0.0/0051105/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... 23920 bright wm thresholded. 3496 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.orig... computing class statistics... border white: 249299 voxels (1.49%) border gray 297398 voxels (1.77%) WM (96.0): 96.7 +- 9.5 [70.0 --> 110.0] GM (66.0) : 66.1 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.5 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 40.9 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-7.0, GM=62+-7.8 mean inside = 91.5, mean outside = 70.4 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 0.89 +- 0.25 (0.01-->4.82) (max @ vno 55647 --> 60516) face area 0.33 +- 0.15 (0.00-->2.99) mean absolute distance = 0.52 +- 0.75 3129 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 54 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 310 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 27 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 54 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown mean border=75.6, 74 (72) missing vertices, mean dist 0.3 [0.6 (%16.9)->0.5 (%83.1))] %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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.04-->4.67) (max @ vno 55647 --> 60516) face area 0.33 +- 0.16 (0.00-->3.25) mean absolute distance = 0.31 +- 0.51 3164 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2471972.0, rms=8.379 001: dt: 0.5000, sse=1300944.5, rms=5.013 (40.173%) 002: dt: 0.5000, sse=1048867.8, rms=3.952 (21.168%) 003: dt: 0.5000, sse=1027928.8, rms=3.861 (2.295%) 004: dt: 0.5000, sse=987943.6, rms=3.650 (5.458%) rms = 3.80, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=811869.3, rms=2.513 (31.153%) 006: dt: 0.2500, sse=754158.6, rms=2.002 (20.352%) 007: dt: 0.2500, sse=737967.4, rms=1.829 (8.649%) rms = 1.78, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=734779.9, rms=1.784 (2.411%) 009: dt: 0.1250, sse=727528.2, rms=1.681 (5.824%) rms = 1.67, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=724518.6, rms=1.668 (0.763%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 53 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 203 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 25 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 45 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 9 points - only 11.11% unknown deleting segment 12 with 6 points - only 0.00% unknown mean border=79.0, 71 (19) missing vertices, mean dist -0.2 [0.3 (%73.2)->0.2 (%26.8))] %81 local maxima, %14 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 0.90 +- 0.25 (0.10-->4.60) (max @ vno 55647 --> 60516) face area 0.35 +- 0.17 (0.00-->3.43) mean absolute distance = 0.23 +- 0.37 2857 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1309219.0, rms=4.865 011: dt: 0.5000, sse=984835.6, rms=3.323 (31.693%) rms = 3.64, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=845579.6, rms=2.393 (28.004%) 013: dt: 0.2500, sse=787174.4, rms=1.860 (22.257%) 014: dt: 0.2500, sse=765525.8, rms=1.625 (12.628%) 015: dt: 0.2500, sse=758600.6, rms=1.544 (5.012%) 016: dt: 0.2500, sse=754683.2, rms=1.489 (3.579%) rms = 1.46, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=752813.2, rms=1.464 (1.620%) 018: dt: 0.1250, sse=745664.3, rms=1.368 (6.572%) rms = 1.36, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=744962.4, rms=1.362 (0.456%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 55 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 238 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 25 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 50 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown mean border=81.2, 73 (16) missing vertices, mean dist -0.1 [0.3 (%66.6)->0.2 (%33.4))] %86 local maxima, % 9 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 0.90 +- 0.25 (0.07-->4.58) (max @ vno 55647 --> 60516) face area 0.34 +- 0.16 (0.00-->3.04) mean absolute distance = 0.22 +- 0.32 2689 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=902626.7, rms=2.990 rms = 3.08, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=783815.1, rms=2.080 (30.451%) 021: dt: 0.2500, sse=728011.9, rms=1.410 (32.217%) 022: dt: 0.2500, sse=718554.3, rms=1.314 (6.827%) rms = 1.29, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=716124.9, rms=1.293 (1.540%) 024: dt: 0.1250, sse=710596.0, rms=1.217 (5.927%) rms = 1.22, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=710292.1, rms=1.217 (-0.054%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 55 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 4 with 245 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 25 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 48 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 8 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 7 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown mean border=81.9, 78 (16) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))] %88 local maxima, % 7 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-6.0.0/0051105/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=733035.6, rms=1.653 rms = 2.12, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=694949.3, rms=1.122 (32.117%) 027: dt: 0.2500, sse=685699.2, rms=0.911 (18.780%) rms = 0.93, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=683681.3, rms=0.905 (0.658%) positioning took 0.4 minutes generating cortex label... 16 non-cortical segments detected only using segment with 7064 vertices erasing segment 0 (vno[0] = 47676) erasing segment 2 (vno[0] = 66100) erasing segment 3 (vno[0] = 72686) erasing segment 4 (vno[0] = 74955) erasing segment 5 (vno[0] = 77311) erasing segment 6 (vno[0] = 79385) erasing segment 7 (vno[0] = 79404) erasing segment 8 (vno[0] = 81512) erasing segment 9 (vno[0] = 88058) erasing segment 10 (vno[0] = 100480) erasing segment 11 (vno[0] = 101352) erasing segment 12 (vno[0] = 103130) erasing segment 13 (vno[0] = 104099) erasing segment 14 (vno[0] = 108701) erasing segment 15 (vno[0] = 135431) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.area vertex spacing 0.89 +- 0.26 (0.01-->4.56) (max @ vno 55647 --> 60516) face area 0.34 +- 0.16 (0.00-->3.04) 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 8 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.0, 81 (81) missing vertices, mean dist 1.5 [3.8 (%0.0)->2.9 (%100.0))] %11 local maxima, %39 large gradients and %45 min vals, 463 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=28113704.0, rms=32.540 001: dt: 0.0500, sse=24545696.0, rms=30.353 (6.723%) 002: dt: 0.0500, sse=21995768.0, rms=28.687 (5.488%) 003: dt: 0.0500, sse=20056470.0, rms=27.353 (4.653%) 004: dt: 0.0500, sse=18499802.0, rms=26.232 (4.097%) 005: dt: 0.0500, sse=17202020.0, rms=25.260 (3.706%) 006: dt: 0.0500, sse=16088886.0, rms=24.395 (3.424%) 007: dt: 0.0500, sse=15114726.0, rms=23.612 (3.209%) 008: dt: 0.0500, sse=14248342.0, rms=22.893 (3.044%) 009: dt: 0.0500, sse=13468190.0, rms=22.226 (2.915%) 010: dt: 0.0500, sse=12760814.0, rms=21.603 (2.803%) positioning took 0.9 minutes mean border=49.8, 82 (39) missing vertices, mean dist 1.3 [2.0 (%0.0)->2.4 (%100.0))] %12 local maxima, %39 large gradients and %44 min vals, 441 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=13484645.0, rms=22.242 011: dt: 0.0500, sse=12832335.0, rms=21.669 (2.577%) 012: dt: 0.0500, sse=12233040.0, rms=21.129 (2.494%) 013: dt: 0.0500, sse=11681176.0, rms=20.618 (2.415%) 014: dt: 0.0500, sse=11171509.0, rms=20.136 (2.341%) 015: dt: 0.0500, sse=10700127.0, rms=19.678 (2.270%) 016: dt: 0.0500, sse=10263281.0, rms=19.245 (2.202%) 017: dt: 0.0500, sse=9858479.0, rms=18.834 (2.134%) 018: dt: 0.0500, sse=9482811.0, rms=18.445 (2.067%) 019: dt: 0.0500, sse=9133861.0, rms=18.076 (2.002%) 020: dt: 0.0500, sse=8809371.0, rms=17.725 (1.938%) positioning took 0.9 minutes mean border=49.7, 108 (34) missing vertices, mean dist 1.1 [0.1 (%0.7)->2.1 (%99.3))] %13 local maxima, %39 large gradients and %43 min vals, 406 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=8895193.0, rms=17.826 021: dt: 0.0500, sse=8588383.0, rms=17.491 (1.884%) 022: dt: 0.0500, sse=8302878.5, rms=17.172 (1.821%) 023: dt: 0.0500, sse=8035737.0, rms=16.868 (1.768%) 024: dt: 0.0500, sse=7786686.5, rms=16.580 (1.708%) 025: dt: 0.0500, sse=7554331.5, rms=16.307 (1.650%) 026: dt: 0.0500, sse=7336978.5, rms=16.047 (1.595%) 027: dt: 0.0500, sse=7132343.5, rms=15.798 (1.552%) 028: dt: 0.0500, sse=6938094.5, rms=15.557 (1.520%) 029: dt: 0.0500, sse=6753533.0, rms=15.326 (1.489%) 030: dt: 0.0500, sse=6578100.0, rms=15.102 (1.459%) positioning took 0.9 minutes mean border=49.6, 147 (26) missing vertices, mean dist 1.0 [0.1 (%6.8)->1.9 (%93.2))] %13 local maxima, %39 large gradients and %43 min vals, 370 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=6663554.5, rms=15.212 031: dt: 0.5000, sse=5403962.5, rms=13.512 (11.175%) 032: dt: 0.5000, sse=4523226.0, rms=12.176 (9.888%) 033: dt: 0.5000, sse=3826992.0, rms=11.006 (9.609%) 034: dt: 0.5000, sse=3261253.0, rms=9.950 (9.596%) 035: dt: 0.5000, sse=2789420.8, rms=8.975 (9.796%) 036: dt: 0.5000, sse=2411856.2, rms=8.110 (9.639%) 037: dt: 0.5000, sse=2105441.5, rms=7.335 (9.558%) 038: dt: 0.5000, sse=1876122.8, rms=6.695 (8.715%) 039: dt: 0.5000, sse=1705520.4, rms=6.179 (7.720%) 040: dt: 0.5000, sse=1598984.1, rms=5.830 (5.634%) 041: dt: 0.5000, sse=1525796.2, rms=5.581 (4.280%) 042: dt: 0.5000, sse=1483706.2, rms=5.430 (2.700%) 043: dt: 0.5000, sse=1454016.1, rms=5.322 (1.989%) 044: dt: 0.5000, sse=1437111.9, rms=5.258 (1.201%) rms = 5.22, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1425933.8, rms=5.217 (0.784%) 046: dt: 0.2500, sse=1346972.9, rms=4.869 (6.668%) 047: dt: 0.2500, sse=1323018.0, rms=4.772 (2.001%) rms = 4.78, time step reduction 2 of 3 to 0.125... rms = 4.75, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1317350.4, rms=4.746 (0.539%) positioning took 2.4 minutes mean border=48.9, 3213 (13) missing vertices, mean dist 0.1 [0.2 (%50.8)->0.6 (%49.2))] %20 local maxima, %34 large gradients and %39 min vals, 186 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=1521424.4, rms=4.759 049: dt: 0.5000, sse=1458198.1, rms=4.506 (5.326%) rms = 4.48, time step reduction 1 of 3 to 0.250... 050: dt: 0.5000, sse=1445987.6, rms=4.480 (0.580%) 051: dt: 0.2500, sse=1377156.9, rms=4.108 (8.306%) 052: dt: 0.2500, sse=1364301.4, rms=4.046 (1.501%) rms = 4.05, time step reduction 2 of 3 to 0.125... rms = 4.01, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=1357532.2, rms=4.009 (0.909%) positioning took 0.9 minutes mean border=48.5, 3399 (12) missing vertices, mean dist 0.1 [0.2 (%51.9)->0.4 (%48.1))] %30 local maxima, %25 large gradients and %38 min vals, 206 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=1395583.9, rms=4.170 rms = 4.51, time step reduction 1 of 3 to 0.250... 054: dt: 0.2500, sse=1369332.5, rms=4.038 (3.183%) rms = 4.05, time step reduction 2 of 3 to 0.125... rms = 4.02, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1366586.8, rms=4.023 (0.369%) positioning took 0.5 minutes mean border=48.0, 6106 (11) missing vertices, mean dist 0.1 [0.2 (%49.0)->0.4 (%51.0))] %35 local maxima, %20 large gradients and %36 min vals, 217 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-6.0.0/0051105/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1399840.4, rms=4.188 rms = 4.16, time step reduction 1 of 3 to 0.250... 056: dt: 0.5000, sse=1386044.1, rms=4.160 (0.670%) 057: dt: 0.2500, sse=1313505.6, rms=3.807 (8.478%) 058: dt: 0.2500, sse=1281807.2, rms=3.653 (4.061%) rms = 3.63, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1277070.1, rms=3.631 (0.598%) 060: dt: 0.1250, sse=1250325.8, rms=3.479 (4.192%) rms = 3.44, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1243304.8, rms=3.443 (1.021%) positioning took 1.0 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.area.pial vertex spacing 1.03 +- 0.45 (0.05-->8.08) (max @ vno 93389 --> 92316) face area 0.41 +- 0.33 (0.00-->4.83) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 135698 vertices processed 25000 of 135698 vertices processed 50000 of 135698 vertices processed 75000 of 135698 vertices processed 100000 of 135698 vertices processed 125000 of 135698 vertices processed 0 of 135698 vertices processed 25000 of 135698 vertices processed 50000 of 135698 vertices processed 75000 of 135698 vertices processed 100000 of 135698 vertices processed 125000 of 135698 vertices processed thickness calculation complete, 99:590 truncations. 27587 vertices at 0 distance 93341 vertices at 1 distance 84964 vertices at 2 distance 36452 vertices at 3 distance 11683 vertices at 4 distance 3418 vertices at 5 distance 1119 vertices at 6 distance 396 vertices at 7 distance 158 vertices at 8 distance 83 vertices at 9 distance 67 vertices at 10 distance 56 vertices at 11 distance 46 vertices at 12 distance 28 vertices at 13 distance 18 vertices at 14 distance 24 vertices at 15 distance 14 vertices at 16 distance 14 vertices at 17 distance 9 vertices at 18 distance 9 vertices at 19 distance 6 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.thickness positioning took 14.6 minutes PIDs (17723 17726) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 01:14:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label Total face volume 256923 Total vertex volume 252720 (mask=0) #@# 0051105 lh 252720 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 01:14:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label Total face volume 253688 Total vertex volume 250027 (mask=0) #@# 0051105 rh 250027 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 01:14:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 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 = 112 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/ribbon.mgz mris_volmask took 12.08 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 01:26:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 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 0051105 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 01:26:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 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 0051105 rh pial Waiting for PID 19028 of (19028 19031 19034 19037) to complete... Waiting for PID 19031 of (19028 19031 19034 19037) to complete... Waiting for PID 19034 of (19028 19031 19034 19037) to complete... Waiting for PID 19037 of (19028 19031 19034 19037) 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 0051105 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923 Total vertex volume 252720 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1360 960 2364 2.566 0.482 0.115 0.022 11 1.3 bankssts 898 597 1491 2.324 0.696 0.129 0.023 15 0.8 caudalanteriorcingulate 3647 2465 7878 2.833 0.500 0.116 0.027 36 3.6 caudalmiddlefrontal 2302 1556 3125 1.950 0.552 0.162 0.045 40 4.6 cuneus 434 292 1622 3.684 0.955 0.106 0.024 4 0.4 entorhinal 4723 3209 10068 2.754 0.666 0.134 0.031 66 6.0 fusiform 7667 5132 14825 2.578 0.511 0.127 0.028 99 8.5 inferiorparietal 5354 3586 11981 2.794 0.613 0.136 0.034 85 7.6 inferiortemporal 1558 1022 3047 2.557 0.815 0.133 0.034 23 2.1 isthmuscingulate 8151 5333 12202 2.079 0.547 0.146 0.042 123 13.4 lateraloccipital 3756 2485 7380 2.795 0.613 0.133 0.032 51 4.8 lateralorbitofrontal 4073 2776 6111 2.049 0.625 0.153 0.044 68 7.3 lingual 2325 1615 5107 2.653 0.666 0.129 0.033 38 3.0 medialorbitofrontal 4371 3015 11420 3.051 0.679 0.131 0.027 65 5.0 middletemporal 851 602 1754 2.541 0.596 0.092 0.021 5 0.7 parahippocampal 2733 1679 5068 2.784 0.572 0.115 0.027 29 2.7 paracentral 2287 1555 5022 2.799 0.543 0.125 0.029 26 2.8 parsopercularis 1071 715 2901 2.998 0.706 0.161 0.051 22 2.3 parsorbitalis 1833 1244 3996 2.725 0.537 0.116 0.025 21 1.8 parstriangularis 1996 1352 2142 1.770 0.451 0.148 0.044 26 3.4 pericalcarine 7126 4640 11191 2.108 0.642 0.116 0.026 78 7.1 postcentral 1931 1266 3777 2.556 0.804 0.131 0.031 31 2.4 posteriorcingulate 7702 4850 14581 2.629 0.682 0.114 0.028 78 9.3 precentral 5136 3501 9228 2.463 0.525 0.125 0.028 63 6.1 precuneus 1054 698 2410 2.984 0.784 0.153 0.047 30 1.7 rostralanteriorcingulate 9184 6424 19015 2.520 0.566 0.133 0.035 140 13.3 rostralmiddlefrontal 9722 6569 22806 2.974 0.579 0.126 0.028 111 10.9 superiorfrontal 7800 5189 12758 2.218 0.535 0.126 0.029 95 8.6 superiorparietal 6317 4234 13786 2.854 0.651 0.119 0.024 69 6.3 superiortemporal 6231 4189 12377 2.678 0.530 0.128 0.029 83 7.1 supramarginal 345 218 989 2.977 0.533 0.154 0.038 8 0.5 frontalpole 584 451 2487 3.948 0.843 0.139 0.035 8 0.8 temporalpole 763 481 1119 2.085 0.512 0.117 0.033 8 0.9 transversetemporal 3371 2234 6683 3.055 0.721 0.118 0.035 38 4.3 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 0051105 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923 Total vertex volume 252720 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1360 916 2364 2.566 0.482 0.127 0.037 27 2.2 bankssts 898 699 1491 2.324 0.696 0.175 0.045 39 1.7 caudalanteriorcingulate 3647 2987 7878 2.833 0.500 0.142 0.034 48 5.6 caudalmiddlefrontal 2302 1828 3125 1.950 0.552 0.164 0.043 37 4.6 cuneus 434 613 1622 3.684 0.955 0.198 0.035 4 0.8 entorhinal 4723 4049 10068 2.754 0.666 0.172 0.045 92 9.8 fusiform 7667 6290 14825 2.578 0.511 0.151 0.033 110 11.7 inferiorparietal 5354 4868 11981 2.794 0.613 0.164 0.038 79 9.5 inferiortemporal 1558 1346 3047 2.557 0.815 0.182 0.050 41 3.6 isthmuscingulate 8151 6459 12202 2.079 0.547 0.145 0.036 110 12.9 lateraloccipital 3756 2939 7380 2.795 0.613 0.152 0.044 64 6.8 lateralorbitofrontal 4073 3401 6111 2.049 0.625 0.170 0.049 74 9.1 lingual 2325 2286 5107 2.653 0.666 0.184 0.045 42 5.0 medialorbitofrontal 4371 4259 11420 3.051 0.679 0.156 0.034 53 6.6 middletemporal 851 793 1754 2.541 0.596 0.140 0.034 6 1.3 parahippocampal 2733 2009 5068 2.784 0.572 0.138 0.036 45 4.4 paracentral 2287 2049 5022 2.799 0.543 0.165 0.043 43 4.4 parsopercularis 1071 1212 2901 2.998 0.706 0.211 0.052 22 2.6 parsorbitalis 1833 1639 3996 2.725 0.537 0.168 0.041 29 3.6 parstriangularis 1996 1163 2142 1.770 0.451 0.130 0.036 32 3.3 pericalcarine 7126 6054 11191 2.108 0.642 0.142 0.030 75 10.2 postcentral 1931 1565 3777 2.556 0.804 0.151 0.041 30 3.6 posteriorcingulate 7702 5978 14581 2.629 0.682 0.126 0.029 91 10.4 precentral 5136 4016 9228 2.463 0.525 0.150 0.038 86 8.7 precuneus 1054 947 2410 2.984 0.784 0.209 0.059 23 3.0 rostralanteriorcingulate 9184 8513 19015 2.520 0.566 0.178 0.042 157 18.9 rostralmiddlefrontal 9722 8501 22806 2.974 0.579 0.158 0.039 148 17.7 superiorfrontal 7800 6192 12758 2.218 0.535 0.143 0.031 107 11.2 superiorparietal 6317 5287 13786 2.854 0.651 0.160 0.041 113 12.2 superiortemporal 6231 5021 12377 2.678 0.530 0.146 0.036 97 9.9 supramarginal 345 427 989 2.977 0.533 0.219 0.046 5 0.9 frontalpole 584 833 2487 3.948 0.843 0.204 0.037 6 1.2 temporalpole 763 637 1119 2.085 0.512 0.156 0.042 10 1.5 transversetemporal 3371 2241 6683 3.055 0.721 0.170 0.057 76 8.9 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 0051105 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688 Total vertex volume 250027 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1135 800 1950 2.547 0.385 0.114 0.020 9 1.0 bankssts 959 659 1925 2.576 0.711 0.139 0.029 17 0.9 caudalanteriorcingulate 3129 2065 6528 2.771 0.550 0.103 0.023 24 2.7 caudalmiddlefrontal 2396 1567 3483 1.969 0.523 0.157 0.048 39 4.6 cuneus 481 365 1571 3.133 0.792 0.125 0.036 4 0.7 entorhinal 4086 2739 8893 2.710 0.659 0.133 0.031 56 5.0 fusiform 8711 5860 16753 2.534 0.555 0.124 0.029 114 9.9 inferiorparietal 4703 3137 10921 2.886 0.694 0.126 0.030 58 5.7 inferiortemporal 1505 979 3063 2.517 0.795 0.126 0.037 21 1.9 isthmuscingulate 7475 4920 11394 2.093 0.566 0.150 0.048 126 15.7 lateraloccipital 3240 2230 6247 2.531 0.669 0.147 0.040 59 5.1 lateralorbitofrontal 4596 3166 7470 2.153 0.577 0.157 0.047 76 8.5 lingual 2803 1906 5585 2.545 0.727 0.132 0.039 52 3.9 medialorbitofrontal 4560 3215 11211 2.837 0.647 0.130 0.027 69 5.1 middletemporal 801 548 1623 2.532 0.615 0.111 0.035 9 0.9 parahippocampal 2425 1585 4382 2.593 0.605 0.113 0.027 22 2.5 paracentral 2137 1496 4791 2.809 0.592 0.116 0.026 21 2.4 parsopercularis 1194 835 3214 2.860 0.596 0.165 0.046 23 2.2 parsorbitalis 2419 1693 4842 2.649 0.547 0.134 0.033 35 3.0 parstriangularis 2420 1595 2658 1.744 0.427 0.147 0.047 33 4.4 pericalcarine 6491 4203 9691 2.037 0.641 0.118 0.030 70 7.3 postcentral 1668 1095 3403 2.605 0.767 0.129 0.031 26 1.9 posteriorcingulate 7370 4611 14605 2.807 0.666 0.112 0.033 70 10.2 precentral 5955 4097 10801 2.442 0.592 0.133 0.029 75 7.0 precuneus 736 481 1634 2.934 0.549 0.154 0.039 18 1.1 rostralanteriorcingulate 9949 6900 19892 2.452 0.589 0.136 0.035 144 14.0 rostralmiddlefrontal 9922 6745 22562 2.857 0.588 0.126 0.030 113 11.5 superiorfrontal 7726 5032 13459 2.331 0.552 0.129 0.032 97 9.4 superiorparietal 5335 3545 11374 2.817 0.587 0.113 0.022 53 4.8 superiortemporal 6233 4211 12356 2.549 0.581 0.123 0.028 78 6.5 supramarginal 503 330 1300 2.962 0.592 0.177 0.059 12 1.5 frontalpole 649 461 2737 3.817 0.636 0.133 0.035 9 0.9 temporalpole 652 426 1040 2.182 0.563 0.169 0.060 14 1.7 transversetemporal 3441 2274 6616 2.921 0.758 0.121 0.037 44 4.5 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 0051105 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688 Total vertex volume 250027 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1135 744 1950 2.547 0.385 0.148 0.045 28 2.4 bankssts 959 825 1925 2.576 0.711 0.171 0.043 27 1.8 caudalanteriorcingulate 3129 2556 6528 2.771 0.550 0.128 0.033 29 4.5 caudalmiddlefrontal 2396 2014 3483 1.969 0.523 0.170 0.048 35 5.1 cuneus 481 583 1571 3.133 0.792 0.220 0.051 9 1.3 entorhinal 4086 3687 8893 2.710 0.659 0.166 0.044 65 8.3 fusiform 8711 7264 16753 2.534 0.555 0.149 0.035 117 13.7 inferiorparietal 4703 4269 10921 2.886 0.694 0.163 0.039 63 8.8 inferiortemporal 1505 1345 3063 2.517 0.795 0.180 0.048 31 3.2 isthmuscingulate 7475 5921 11394 2.093 0.566 0.148 0.039 121 12.7 lateraloccipital 3240 2764 6247 2.531 0.669 0.188 0.052 76 7.8 lateralorbitofrontal 4596 3813 7470 2.153 0.577 0.171 0.049 84 10.6 lingual 2803 2498 5585 2.545 0.727 0.175 0.052 74 6.9 medialorbitofrontal 4560 4608 11211 2.837 0.647 0.167 0.037 62 7.8 middletemporal 801 715 1623 2.532 0.615 0.166 0.044 13 1.7 parahippocampal 2425 1762 4382 2.593 0.605 0.134 0.034 32 3.6 paracentral 2137 1997 4791 2.809 0.592 0.169 0.043 33 4.3 parsopercularis 1194 1425 3214 2.860 0.596 0.213 0.045 24 2.7 parsorbitalis 2419 2082 4842 2.649 0.547 0.176 0.045 52 5.4 parstriangularis 2420 1485 2658 1.744 0.427 0.130 0.035 46 3.9 pericalcarine 6491 5332 9691 2.037 0.641 0.144 0.033 68 10.0 postcentral 1668 1379 3403 2.605 0.767 0.160 0.040 35 3.0 posteriorcingulate 7370 5494 14605 2.807 0.666 0.119 0.027 78 9.0 precentral 5955 4677 10801 2.442 0.592 0.148 0.039 83 10.1 precuneus 736 663 1634 2.934 0.549 0.189 0.048 13 1.8 rostralanteriorcingulate 9949 9108 19892 2.452 0.589 0.175 0.040 158 18.5 rostralmiddlefrontal 9922 8734 22562 2.857 0.588 0.161 0.041 157 18.8 superiorfrontal 7726 6292 13459 2.331 0.552 0.150 0.036 110 12.4 superiorparietal 5335 4552 11374 2.817 0.587 0.164 0.044 98 11.0 superiortemporal 6233 5342 12356 2.549 0.581 0.159 0.038 89 11.3 supramarginal 503 509 1300 2.962 0.592 0.189 0.040 14 0.9 frontalpole 649 956 2737 3.817 0.636 0.236 0.048 10 1.7 temporalpole 652 524 1040 2.182 0.563 0.167 0.057 11 1.6 transversetemporal 3441 2196 6616 2.921 0.758 0.162 0.061 85 9.2 insula PIDs (19028 19031 19034 19037) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 01:28:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 8 01:28:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 19121 of (19121 19124) to complete... Waiting for PID 19124 of (19121 19124) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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... 89 labels changed using aseg relabeling using gibbs priors... 000: 9220 changed, 136564 examined... 001: 2186 changed, 35994 examined... 002: 678 changed, 11492 examined... 003: 290 changed, 3759 examined... 004: 132 changed, 1663 examined... 005: 61 changed, 759 examined... 006: 23 changed, 303 examined... 007: 11 changed, 136 examined... 008: 8 changed, 72 examined... 009: 6 changed, 42 examined... 010: 1 changed, 30 examined... 011: 0 changed, 7 examined... 5 labels changed using aseg 000: 288 total segments, 201 labels (2339 vertices) changed 001: 94 total segments, 7 labels (70 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 45 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 833 vertices marked for relabeling... 833 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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... 45 labels changed using aseg relabeling using gibbs priors... 000: 8807 changed, 135698 examined... 001: 1981 changed, 34813 examined... 002: 565 changed, 10406 examined... 003: 243 changed, 3221 examined... 004: 121 changed, 1363 examined... 005: 50 changed, 699 examined... 006: 27 changed, 320 examined... 007: 9 changed, 139 examined... 008: 6 changed, 58 examined... 009: 3 changed, 37 examined... 010: 2 changed, 16 examined... 011: 2 changed, 13 examined... 012: 1 changed, 15 examined... 013: 0 changed, 5 examined... 14 labels changed using aseg 000: 244 total segments, 158 labels (2304 vertices) changed 001: 92 total segments, 8 labels (25 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 905 vertices marked for relabeling... 905 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. PIDs (19121 19124) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 01:28:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 01:28:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh white Waiting for PID 19172 of (19172 19175) to complete... Waiting for PID 19175 of (19172 19175) 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 0051105 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923 Total vertex volume 252720 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1312 899 2715 2.658 0.499 0.136 0.033 25 1.8 G&S_frontomargin 1506 1010 2607 2.213 0.637 0.145 0.041 21 2.3 G&S_occipital_inf 2145 1229 3828 2.600 0.601 0.117 0.034 28 3.1 G&S_paracentral 1736 1161 3773 2.738 0.582 0.143 0.031 27 2.1 G&S_subcentral 693 471 1769 2.715 0.523 0.153 0.037 16 0.9 G&S_transv_frontopol 1924 1350 4105 2.918 0.602 0.130 0.033 35 2.2 G&S_cingul-Ant 1217 859 2350 2.746 0.455 0.122 0.025 15 1.2 G&S_cingul-Mid-Ant 1535 1048 3226 2.850 0.513 0.125 0.032 19 1.9 G&S_cingul-Mid-Post 733 493 1966 2.994 0.492 0.157 0.039 14 1.1 G_cingul-Post-dorsal 415 282 1205 3.032 0.839 0.158 0.049 7 0.8 G_cingul-Post-ventral 2018 1381 2772 1.811 0.523 0.162 0.044 35 3.8 G_cuneus 1393 938 3883 2.942 0.555 0.132 0.032 20 2.0 G_front_inf-Opercular 484 301 1228 2.968 0.503 0.140 0.040 9 0.8 G_front_inf-Orbital 1124 749 2852 2.845 0.478 0.132 0.036 19 1.4 G_front_inf-Triangul 4921 3398 13040 2.820 0.606 0.145 0.043 94 8.7 G_front_middle 6716 4403 18328 3.178 0.553 0.134 0.032 91 8.3 G_front_sup 783 497 1500 2.867 0.771 0.131 0.058 15 1.5 G_Ins_lg&S_cent_ins 677 437 1932 3.420 0.748 0.124 0.033 10 0.8 G_insular_short 2719 1733 5756 2.571 0.568 0.149 0.042 52 4.2 G_occipital_middle 1461 983 2256 1.962 0.525 0.150 0.044 23 2.5 G_occipital_sup 1972 1266 4867 3.017 0.652 0.146 0.037 37 2.7 G_oc-temp_lat-fusifor 2790 1865 4380 2.016 0.671 0.175 0.057 62 6.3 G_oc-temp_med-Lingual 993 659 2875 3.098 0.925 0.102 0.030 9 1.2 G_oc-temp_med-Parahip 2494 1626 6064 2.786 0.748 0.148 0.043 48 4.4 G_orbital 2835 1888 6945 2.803 0.501 0.142 0.035 50 4.0 G_pariet_inf-Angular 3069 2015 6946 2.761 0.570 0.137 0.033 49 3.9 G_pariet_inf-Supramar 2938 1922 5849 2.447 0.533 0.134 0.033 45 3.5 G_parietal_sup 2875 1766 4962 2.209 0.584 0.120 0.034 38 3.5 G_postcentral 3071 1804 6830 2.862 0.688 0.111 0.031 34 4.2 G_precentral 2465 1676 5768 2.653 0.560 0.142 0.036 46 3.6 G_precuneus 997 677 2830 2.861 0.679 0.144 0.050 24 2.0 G_rectus 160 106 345 2.993 0.796 0.102 0.036 2 0.1 G_subcallosal 541 345 953 2.166 0.545 0.111 0.036 6 0.7 G_temp_sup-G_T_transv 2131 1399 6336 3.118 0.573 0.140 0.035 38 3.1 G_temp_sup-Lateral 720 524 2076 3.323 0.934 0.100 0.023 4 0.6 G_temp_sup-Plan_polar 1178 804 2574 2.900 0.514 0.108 0.018 11 0.7 G_temp_sup-Plan_tempo 2977 1941 7918 2.979 0.615 0.148 0.043 64 5.4 G_temporal_inf 2256 1559 7181 3.270 0.605 0.145 0.034 43 3.0 G_temporal_middle 264 177 435 2.604 0.598 0.078 0.012 1 0.1 Lat_Fis-ant-Horizont 322 223 490 2.508 0.464 0.100 0.013 2 0.2 Lat_Fis-ant-Vertical 1274 861 1788 2.701 0.529 0.134 0.030 18 1.6 Lat_Fis-post 2478 1615 3292 1.829 0.458 0.162 0.055 48 5.6 Pole_occipital 1519 1105 5622 3.519 0.806 0.142 0.032 23 2.1 Pole_temporal 2654 1784 2914 1.877 0.485 0.133 0.036 29 4.0 S_calcarine 2889 1982 3051 1.734 0.547 0.116 0.022 21 2.7 S_central 1251 849 1940 2.534 0.450 0.114 0.022 13 1.2 S_cingul-Marginalis 482 340 834 2.990 0.346 0.114 0.025 4 0.5 S_circular_insula_ant 1242 866 2071 2.922 0.741 0.099 0.017 6 0.9 S_circular_insula_inf 1792 1212 2867 2.876 0.556 0.102 0.018 9 1.3 S_circular_insula_sup 1023 701 1708 2.536 0.464 0.122 0.026 13 1.1 S_collat_transv_ant 422 298 438 1.810 0.366 0.135 0.029 4 0.5 S_collat_transv_post 2356 1639 3673 2.315 0.428 0.110 0.020 16 1.9 S_front_inf 1979 1423 3245 2.362 0.436 0.125 0.033 18 2.6 S_front_middle 2775 1901 4624 2.561 0.465 0.107 0.022 17 2.5 S_front_sup 425 310 703 2.504 0.387 0.127 0.022 3 0.5 S_interm_prim-Jensen 2563 1742 3421 2.112 0.399 0.110 0.019 21 2.2 S_intrapariet&P_trans 1438 957 1660 1.996 0.398 0.125 0.031 12 1.8 S_oc_middle&Lunatus 1567 1068 2085 2.167 0.379 0.119 0.020 15 1.2 S_oc_sup&transversal 656 465 1069 2.281 0.389 0.116 0.021 6 0.6 S_occipital_ant 1118 775 1700 2.252 0.490 0.121 0.026 11 1.3 S_oc-temp_lat 2021 1429 3118 2.452 0.487 0.109 0.019 12 1.6 S_oc-temp_med&Lingual 356 251 572 2.445 0.520 0.139 0.029 3 0.5 S_orbital_lateral 688 460 928 2.414 0.588 0.111 0.017 5 0.4 S_orbital_med-olfact 1295 871 2498 3.001 0.494 0.129 0.028 14 1.4 S_orbital-H_Shaped 2112 1417 2953 2.309 0.452 0.108 0.022 15 2.1 S_parieto_occipital 1418 801 1215 1.808 0.745 0.119 0.024 25 1.2 S_pericallosal 3517 2357 4746 2.164 0.481 0.108 0.020 25 2.9 S_postcentral 1455 989 2366 2.632 0.424 0.110 0.021 10 1.1 S_precentral-inf-part 1525 1043 2537 2.523 0.443 0.101 0.021 9 1.3 S_precentral-sup-part 581 425 809 2.284 0.403 0.128 0.021 6 0.5 S_suborbital 812 570 1232 2.481 0.355 0.111 0.024 6 0.7 S_subparietal 1657 1161 2575 2.647 0.531 0.118 0.020 12 1.4 S_temporal_inf 6262 4264 10173 2.536 0.456 0.110 0.021 51 5.2 S_temporal_sup 501 343 577 2.067 0.417 0.125 0.017 5 0.4 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 0051105 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688 Total vertex volume 250027 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 801 549 1692 2.664 0.624 0.152 0.048 14 1.7 G&S_frontomargin 1263 821 2186 2.341 0.565 0.129 0.031 15 1.5 G&S_occipital_inf 1579 967 2792 2.365 0.591 0.130 0.044 24 2.7 G&S_paracentral 1549 1055 3238 2.543 0.698 0.140 0.034 21 2.0 G&S_subcentral 1272 901 3108 2.765 0.636 0.165 0.043 28 2.1 G&S_transv_frontopol 2731 1875 5565 2.839 0.568 0.140 0.034 49 3.4 G&S_cingul-Ant 1125 796 2358 2.778 0.471 0.106 0.022 9 0.9 G&S_cingul-Mid-Ant 1421 974 2925 2.828 0.552 0.123 0.029 15 1.7 G&S_cingul-Mid-Post 560 374 1738 3.129 0.564 0.154 0.054 12 1.1 G_cingul-Post-dorsal 386 277 1215 2.985 0.660 0.157 0.056 8 0.8 G_cingul-Post-ventral 2215 1456 3094 1.856 0.469 0.157 0.048 36 4.2 G_cuneus 1392 955 4030 3.024 0.621 0.130 0.031 20 1.9 G_front_inf-Opercular 483 333 1367 2.911 0.536 0.151 0.043 10 0.6 G_front_inf-Orbital 1065 754 2484 2.596 0.506 0.149 0.042 23 1.6 G_front_inf-Triangul 4830 3283 12632 2.768 0.605 0.147 0.042 89 8.0 G_front_middle 6783 4498 17193 2.936 0.578 0.133 0.034 93 8.8 G_front_sup 593 428 1304 2.828 0.866 0.138 0.041 11 0.8 G_Ins_lg&S_cent_ins 798 481 2007 3.047 1.038 0.132 0.056 16 1.5 G_insular_short 2699 1755 5581 2.578 0.659 0.154 0.043 53 4.1 G_occipital_middle 1552 964 2842 2.263 0.551 0.143 0.042 23 2.4 G_occipital_sup 1826 1155 4558 2.886 0.573 0.151 0.041 36 2.9 G_oc-temp_lat-fusifor 2964 2027 5450 2.196 0.613 0.168 0.055 57 6.6 G_oc-temp_med-Lingual 1088 773 3170 2.970 0.780 0.123 0.044 12 1.5 G_oc-temp_med-Parahip 2553 1734 6454 2.676 0.757 0.164 0.051 63 5.4 G_orbital 3360 2215 7791 2.643 0.552 0.139 0.037 62 4.8 G_pariet_inf-Angular 2904 1961 6795 2.739 0.591 0.139 0.035 50 3.9 G_pariet_inf-Supramar 2387 1562 5146 2.547 0.601 0.140 0.037 38 3.1 G_parietal_sup 2370 1442 3855 2.091 0.565 0.125 0.038 32 3.3 G_postcentral 2745 1537 6952 3.218 0.514 0.112 0.043 32 4.9 G_precentral 2600 1740 6020 2.706 0.569 0.154 0.039 49 4.0 G_precuneus 711 484 1853 2.446 0.847 0.153 0.065 19 1.7 G_rectus 393 246 691 2.632 0.931 0.092 0.036 6 0.4 G_subcallosal 459 294 903 2.318 0.716 0.162 0.058 10 0.9 G_temp_sup-G_T_transv 1725 1102 4718 3.041 0.545 0.129 0.026 25 1.9 G_temp_sup-Lateral 881 607 2134 3.091 0.763 0.080 0.021 5 0.6 G_temp_sup-Plan_polar 879 600 1852 2.704 0.572 0.104 0.022 7 0.8 G_temp_sup-Plan_tempo 2430 1654 7329 3.155 0.650 0.143 0.039 45 3.8 G_temporal_inf 2610 1809 7573 2.960 0.645 0.144 0.034 56 3.7 G_temporal_middle 315 229 481 2.804 0.367 0.103 0.016 1 0.2 Lat_Fis-ant-Horizont 279 187 468 2.771 0.614 0.099 0.024 1 0.2 Lat_Fis-ant-Vertical 1502 1003 2134 2.532 0.467 0.116 0.025 12 1.8 Lat_Fis-post 3293 2218 5125 1.996 0.587 0.169 0.054 64 7.0 Pole_occipital 1796 1176 6153 3.419 0.697 0.131 0.031 24 2.3 Pole_temporal 2744 1857 2917 1.822 0.459 0.146 0.041 37 4.6 S_calcarine 2960 1986 3211 1.871 0.616 0.109 0.023 19 3.0 S_central 1345 965 2125 2.423 0.530 0.096 0.015 6 0.8 S_cingul-Marginalis 542 368 868 2.820 0.618 0.117 0.024 3 0.6 S_circular_insula_ant 1069 730 1647 2.790 0.647 0.095 0.017 5 0.8 S_circular_insula_inf 1501 1003 2267 2.812 0.510 0.103 0.021 8 1.4 S_circular_insula_sup 1108 760 1737 2.466 0.517 0.098 0.015 6 0.7 S_collat_transv_ant 256 189 360 2.450 0.599 0.151 0.030 2 0.3 S_collat_transv_post 2516 1742 4197 2.327 0.511 0.111 0.022 23 2.4 S_front_inf 2487 1710 3463 2.198 0.451 0.110 0.022 16 2.2 S_front_middle 2509 1719 4156 2.496 0.541 0.105 0.025 16 2.4 S_front_sup 636 428 825 2.291 0.480 0.102 0.017 3 0.6 S_interm_prim-Jensen 3359 2244 4740 2.162 0.454 0.115 0.024 29 3.1 S_intrapariet&P_trans 979 668 1048 1.824 0.435 0.134 0.078 16 4.7 S_oc_middle&Lunatus 1407 934 1681 2.015 0.386 0.122 0.027 14 1.6 S_oc_sup&transversal 645 439 915 2.084 0.403 0.116 0.027 6 0.7 S_occipital_ant 1157 794 1671 2.255 0.433 0.111 0.020 9 0.9 S_oc-temp_lat 1694 1195 2446 2.383 0.470 0.111 0.019 12 1.3 S_oc-temp_med&Lingual 615 429 872 2.287 0.473 0.139 0.034 7 0.8 S_orbital_lateral 559 395 879 2.580 0.656 0.098 0.017 3 0.3 S_orbital_med-olfact 1161 825 2086 2.530 0.532 0.144 0.033 14 1.5 S_orbital-H_Shaped 2447 1622 3498 2.261 0.546 0.115 0.024 20 2.5 S_parieto_occipital 1281 775 1073 1.785 0.580 0.127 0.018 21 0.8 S_pericallosal 3186 2095 4815 2.287 0.516 0.108 0.021 25 2.7 S_postcentral 1740 1200 2870 2.711 0.502 0.096 0.017 9 1.2 S_precentral-inf-part 1506 1026 2302 2.546 0.537 0.102 0.017 7 1.2 S_precentral-sup-part 347 243 582 2.710 0.694 0.152 0.026 4 0.4 S_suborbital 1216 842 1915 2.428 0.458 0.112 0.020 8 1.0 S_subparietal 1342 940 1986 2.523 0.508 0.124 0.025 10 1.4 S_temporal_inf 5938 4127 9416 2.489 0.460 0.109 0.019 45 4.7 S_temporal_sup 387 273 506 2.343 0.633 0.151 0.025 4 0.4 S_temporal_transverse PIDs (19172 19175) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 01:29:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 8 01:29:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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 19235 of (19235 19238) to complete... Waiting for PID 19238 of (19235 19238) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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... 1240 labels changed using aseg relabeling using gibbs priors... 000: 1979 changed, 136564 examined... 001: 456 changed, 9305 examined... 002: 124 changed, 2675 examined... 003: 49 changed, 755 examined... 004: 29 changed, 273 examined... 005: 15 changed, 170 examined... 006: 7 changed, 82 examined... 007: 4 changed, 49 examined... 008: 4 changed, 26 examined... 009: 2 changed, 24 examined... 010: 2 changed, 12 examined... 011: 1 changed, 10 examined... 012: 1 changed, 7 examined... 013: 0 changed, 7 examined... 203 labels changed using aseg 000: 57 total segments, 24 labels (176 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 742 vertices marked for relabeling... 742 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051105 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... 1360 labels changed using aseg relabeling using gibbs priors... 000: 1943 changed, 135698 examined... 001: 451 changed, 9077 examined... 002: 129 changed, 2550 examined... 003: 56 changed, 780 examined... 004: 28 changed, 342 examined... 005: 20 changed, 165 examined... 006: 17 changed, 101 examined... 007: 7 changed, 95 examined... 008: 6 changed, 43 examined... 009: 4 changed, 31 examined... 010: 2 changed, 24 examined... 011: 1 changed, 14 examined... 012: 0 changed, 9 examined... 184 labels changed using aseg 000: 52 total segments, 19 labels (64 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... 692 vertices marked for relabeling... 692 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. PIDs (19235 19238) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 01:29:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 01:29:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh white Waiting for PID 19285 of (19285 19288) to complete... Waiting for PID 19288 of (19285 19288) 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 0051105 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 256923 Total vertex volume 252720 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1463 978 2473 2.480 0.636 0.126 0.023 22 1.4 caudalanteriorcingulate 3916 2648 8515 2.846 0.496 0.117 0.027 39 3.9 caudalmiddlefrontal 3014 2041 4269 2.027 0.550 0.145 0.038 43 5.1 cuneus 452 300 1627 3.617 0.979 0.104 0.024 4 0.4 entorhinal 4240 2870 8640 2.721 0.648 0.134 0.032 61 5.4 fusiform 7704 5172 14890 2.596 0.514 0.127 0.028 98 8.4 inferiorparietal 5336 3610 12642 2.831 0.643 0.134 0.033 81 7.1 inferiortemporal 1558 1024 3042 2.567 0.809 0.133 0.035 22 2.1 isthmuscingulate 8209 5361 12313 2.074 0.556 0.145 0.042 123 13.4 lateraloccipital 4111 2682 8461 2.815 0.635 0.132 0.033 62 5.3 lateralorbitofrontal 4196 2855 6198 2.042 0.619 0.153 0.044 71 7.4 lingual 1835 1271 4078 2.632 0.689 0.125 0.033 29 2.4 medialorbitofrontal 5804 3983 13688 2.910 0.659 0.128 0.028 82 6.8 middletemporal 907 637 1848 2.532 0.594 0.091 0.021 5 0.8 parahippocampal 3095 1910 6018 2.829 0.567 0.117 0.027 33 3.2 paracentral 2074 1411 4506 2.810 0.549 0.127 0.030 24 2.6 parsopercularis 990 674 2583 3.163 0.607 0.141 0.038 15 1.5 parsorbitalis 2341 1584 4808 2.663 0.506 0.115 0.025 28 2.3 parstriangularis 2048 1392 2283 1.783 0.458 0.152 0.047 28 3.9 pericalcarine 8110 5291 12596 2.143 0.638 0.120 0.027 91 8.4 postcentral 2181 1424 4330 2.591 0.767 0.131 0.031 35 2.7 posteriorcingulate 7709 4821 14563 2.635 0.682 0.113 0.029 78 9.4 precentral 5024 3437 9247 2.446 0.551 0.127 0.029 65 6.0 precuneus 1383 924 3000 2.939 0.737 0.149 0.042 33 2.0 rostralanteriorcingulate 7067 4969 15148 2.502 0.590 0.139 0.039 114 11.6 rostralmiddlefrontal 10553 7201 24271 2.892 0.608 0.128 0.029 126 12.0 superiorfrontal 6095 4047 10040 2.230 0.517 0.124 0.028 75 6.6 superiorparietal 8043 5457 18573 2.906 0.733 0.123 0.027 94 9.1 superiortemporal 5607 3781 11109 2.677 0.531 0.126 0.028 74 6.2 supramarginal 799 504 1151 2.081 0.506 0.119 0.032 8 0.9 transversetemporal 2799 1876 5810 3.123 0.680 0.114 0.029 28 2.9 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 0051105 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 253688 Total vertex volume 250027 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1004 692 1985 2.555 0.712 0.139 0.029 17 1.0 caudalanteriorcingulate 3309 2196 6786 2.751 0.554 0.104 0.022 25 2.8 caudalmiddlefrontal 2835 1856 4063 1.962 0.512 0.147 0.044 41 5.0 cuneus 442 343 1415 3.098 0.798 0.128 0.038 4 0.6 entorhinal 3672 2479 7635 2.660 0.589 0.131 0.031 48 4.5 fusiform 8728 5848 16748 2.529 0.556 0.125 0.030 114 10.1 inferiorparietal 5156 3429 12513 2.904 0.739 0.128 0.029 68 6.2 inferiortemporal 1478 961 2979 2.527 0.786 0.123 0.034 19 1.7 isthmuscingulate 7485 4917 11396 2.094 0.573 0.150 0.048 123 15.7 lateraloccipital 3703 2522 7439 2.500 0.680 0.150 0.047 77 6.5 lateralorbitofrontal 4548 3133 7390 2.158 0.577 0.158 0.047 76 8.5 lingual 2012 1350 4327 2.581 0.761 0.137 0.048 42 3.6 medialorbitofrontal 5477 3854 12751 2.800 0.619 0.129 0.027 79 6.1 middletemporal 875 600 1747 2.527 0.594 0.112 0.034 10 1.0 parahippocampal 2569 1672 4665 2.588 0.601 0.114 0.027 24 2.8 paracentral 2443 1716 5369 2.763 0.601 0.117 0.027 26 2.8 parsopercularis 1009 698 2588 2.951 0.558 0.144 0.032 14 1.3 parsorbitalis 2624 1803 5107 2.629 0.511 0.132 0.033 38 3.2 parstriangularis 2377 1561 2646 1.759 0.440 0.147 0.047 33 4.4 pericalcarine 7115 4609 10852 2.072 0.650 0.117 0.029 75 7.9 postcentral 1784 1168 3628 2.602 0.755 0.130 0.031 28 2.1 posteriorcingulate 7115 4458 14201 2.818 0.660 0.112 0.033 68 9.8 precentral 6133 4243 11348 2.447 0.581 0.136 0.030 83 7.5 precuneus 1074 717 2208 2.853 0.658 0.145 0.034 23 1.4 rostralanteriorcingulate 7260 5020 14496 2.443 0.593 0.140 0.036 106 11.0 rostralmiddlefrontal 12745 8718 28382 2.783 0.612 0.129 0.031 158 15.4 superiorfrontal 6396 4152 11045 2.332 0.552 0.130 0.032 82 7.7 superiorparietal 6818 4590 15587 2.878 0.664 0.115 0.024 68 6.6 superiortemporal 5947 4015 11748 2.560 0.585 0.124 0.028 74 6.3 supramarginal 659 427 1063 2.202 0.574 0.164 0.058 14 1.7 transversetemporal 3014 2026 5921 2.974 0.740 0.118 0.029 31 3.4 insula PIDs (19285 19288) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 01:29:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts pctsurfcon --s 0051105 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 01:29:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts pctsurfcon --s 0051105 --rh-only Waiting for PID 19350 of (19350 19362) to complete... Waiting for PID 19362 of (19350 19362) to complete... pctsurfcon --s 0051105 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts/pctsurfcon.log Sun Oct 8 01:29:54 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-967 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-6.0.0/0051105/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.wm.mgh --regheader 0051105 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 65062 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.wm.mgh Dim: 136564 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.gm.mgh --projfrac 0.3 --regheader 0051105 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 80207 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.gm.mgh Dim: 136564 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19350/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.w-g.pct.mgh --annot 0051105 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/lh.w-g.pct.mgh --annot 0051105 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-967 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/lh.w-g.pct.mgh Vertex Area is 0.667487 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 0051105 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/scripts/pctsurfcon.log Sun Oct 8 01:29:54 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-967 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-6.0.0/0051105/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.wm.mgh --regheader 0051105 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 64817 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.wm.mgh Dim: 135698 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.gm.mgh --projfrac 0.3 --regheader 0051105 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 80080 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.gm.mgh Dim: 135698 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/tmp.pctsurfcon.19362/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.w-g.pct.mgh --annot 0051105 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.w-g.pct.mgh --annot 0051105 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-967 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.w-g.pct.mgh Vertex Area is 0.669006 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 (19350 19362) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 01:30:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 735 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 643 voxels changed to hypointensity... 1529 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 01:30:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 mri_aparc2aseg --s 0051105 --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 8 01:30:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 mri_aparc2aseg --s 0051105 --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 8 01:30:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 mri_aparc2aseg --s 0051105 --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 19543 of (19543 19546 19549) to complete... Waiting for PID 19546 of (19543 19546 19549) to complete... Waiting for PID 19549 of (19543 19546 19549) to complete... mri_aparc2aseg --s 0051105 --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 0051105 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/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 6.14 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 63 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 88 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 7 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 55 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 56 rescaling Left_VentralDC from 87 --> 83 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 53 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 54 rescaling Right_Thalamus_Proper from 85 --> 80 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 86 rescaling Right_Hippocampus from 53 --> 53 rescaling Right_Amygdala from 55 --> 54 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 87 rescaling Fifth_Ventricle from 40 --> 17 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 498595 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 191 changed. pass 2: 9 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc+aseg.mgz mri_aparc2aseg --s 0051105 --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 0051105 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/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 6.14 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 63 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 88 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 7 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 55 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 56 rescaling Left_VentralDC from 87 --> 83 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 53 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 54 rescaling Right_Thalamus_Proper from 85 --> 80 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 86 rescaling Right_Hippocampus from 53 --> 53 rescaling Right_Amygdala from 55 --> 54 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 87 rescaling Fifth_Ventricle from 40 --> 17 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 498605 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 191 changed. pass 2: 9 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0051105 --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 0051105 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/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-6.0.0/0051105/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 6.14 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 63 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 88 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 7 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 55 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 56 rescaling Left_VentralDC from 87 --> 83 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 53 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 86 rescaling Right_Cerebellum_Cortex from 59 --> 54 rescaling Right_Thalamus_Proper from 85 --> 80 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 73 rescaling Right_Pallidum from 97 --> 86 rescaling Right_Hippocampus from 53 --> 53 rescaling Right_Amygdala from 55 --> 54 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 87 rescaling Fifth_Ventricle from 40 --> 17 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 498605 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 191 changed. pass 2: 9 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (19543 19546 19549) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 01:37:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 01:37:43 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-967 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-6.0.0/0051105/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-967 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 8 01:37:43 CEST 2017 Ended at Sun Oct 8 01:37:50 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 01:37:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 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 0051105 $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 0051105 sysname Linux hostname tars-967 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1405286 mm^3 (det: 1.386270 ) Computing euler number orig.nofix lheno = -78, rheno = -62 orig.nofix lhholes = 40, rhholes = 32 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 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 8 01:39:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105 mri_aparc2aseg --s 0051105 --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 0051105 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-6.0.0/0051105/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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-6.0.0/0051105/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7908 vertices from left hemi Ripped 7893 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-6.0.0/0051105/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 = 920498 Used brute-force search on 303 voxels Fixing Parahip LH WM Found 16 clusters 0 k 2.000000 1 k 88.000000 2 k 1.000000 3 k 1.000000 4 k 1092.000000 5 k 1.000000 6 k 5.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 25.000000 11 k 1.000000 12 k 2.000000 13 k 1.000000 14 k 1.000000 15 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 3.000000 1 k 5.000000 2 k 1.000000 3 k 1.000000 4 k 1102.000000 5 k 7.000000 6 k 1.000000 7 k 2.000000 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 0051105 --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 0051105 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-967 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1405286 mm^3 (det: 1.386270 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 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-6.0.0/0051105/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 01:48:41 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 20686 of (20686 20692 20698 20704 20708) to complete... Waiting for PID 20692 of (20686 20692 20698 20704 20708) to complete... Waiting for PID 20698 of (20686 20692 20698 20704 20708) to complete... Waiting for PID 20704 of (20686 20692 20698 20704 20708) to complete... Waiting for PID 20708 of (20686 20692 20698 20704 20708) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 576 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4705 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 952 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8861 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4260 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 415 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6398 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 748 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6532 mri_label2label: Done PIDs (20686 20692 20698 20704 20708) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 20756 of (20756 20762 20768 20773) to complete... Waiting for PID 20762 of (20756 20762 20768 20773) to complete... Waiting for PID 20768 of (20756 20762 20768 20773) to complete... Waiting for PID 20773 of (20756 20762 20768 20773) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 365 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4435 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 1175 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14764 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4419 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 642 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4064 mri_label2label: Done PIDs (20756 20762 20768 20773) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 20831 of (20831 20837 20843 20848 20854) to complete... Waiting for PID 20837 of (20831 20837 20843 20848 20854) to complete... Waiting for PID 20843 of (20831 20837 20843 20848 20854) to complete... Waiting for PID 20848 of (20831 20837 20843 20848 20854) to complete... Waiting for PID 20854 of (20831 20837 20843 20848 20854) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 1560 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6201 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 2755 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10869 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 471 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2489 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1324 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1223 mri_label2label: Done PIDs (20831 20837 20843 20848 20854) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 20903 of (20903 20909 20915 20921 20927) to complete... Waiting for PID 20909 of (20903 20909 20915 20921 20927) to complete... Waiting for PID 20915 of (20903 20909 20915 20921 20927) to complete... Waiting for PID 20921 of (20903 20909 20915 20921 20927) to complete... Waiting for PID 20927 of (20903 20909 20915 20921 20927) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1154 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 389 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2481 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1559 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2091 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 395 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2714 mri_label2label: Done PIDs (20903 20909 20915 20921 20927) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 21002 of (21002 21008 21014 21020) to complete... Waiting for PID 21008 of (21002 21008 21014 21020) to complete... Waiting for PID 21014 of (21002 21008 21014 21020) to complete... Waiting for PID 21020 of (21002 21008 21014 21020) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1633 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 467 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7502 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2042 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1400 mri_label2label: Done PIDs (21002 21008 21014 21020) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 21064 of (21064 21070 21076 21082 21088) to complete... Waiting for PID 21070 of (21064 21070 21076 21082 21088) to complete... Waiting for PID 21076 of (21064 21070 21076 21082 21088) to complete... Waiting for PID 21082 of (21064 21070 21076 21082 21088) to complete... Waiting for PID 21088 of (21064 21070 21076 21082 21088) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 1039 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4444 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 1403 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4737 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 590 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 483 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 136564 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 453 mri_label2label: Done PIDs (21064 21070 21076 21082 21088) completed and logs appended. mris_label2annot --s 0051105 --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-6.0.0/0051105/label cmdline mris_label2annot --s 0051105 --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-967 machine x86_64 user ntraut subject 0051105 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-6.0.0/0051105/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 94361 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/lh.BA_exvivo.annot mris_label2annot --s 0051105 --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-6.0.0/0051105/label cmdline mris_label2annot --s 0051105 --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-967 machine x86_64 user ntraut subject 0051105 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-6.0.0/0051105/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 111447 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 256923 Total vertex volume 252720 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1301 768 2426 2.305 0.576 0.131 0.042 22 1.9 BA1_exvivo 4705 3136 7467 2.273 0.526 0.111 0.022 39 4.1 BA2_exvivo 1038 688 894 1.608 0.419 0.137 0.030 10 1.2 BA3a_exvivo 2447 1587 3295 1.872 0.648 0.114 0.026 26 2.5 BA3b_exvivo 2110 1156 3874 2.848 0.582 0.111 0.032 22 3.0 BA4a_exvivo 1321 849 1916 2.337 0.651 0.111 0.027 9 1.6 BA4p_exvivo 9069 5941 20233 2.876 0.567 0.118 0.029 97 10.1 BA6_exvivo 2108 1442 5099 2.872 0.545 0.126 0.029 25 2.5 BA44_exvivo 2992 2052 6162 2.596 0.519 0.124 0.028 38 3.2 BA45_exvivo 3720 2536 4235 1.708 0.460 0.152 0.047 56 7.3 V1_exvivo 8285 5484 11624 1.964 0.548 0.159 0.048 144 16.3 V2_exvivo 2087 1375 4077 2.468 0.537 0.137 0.033 29 2.6 MT_exvivo 478 306 1494 3.399 0.878 0.097 0.024 4 0.4 perirhinal_exvivo 542 383 1402 2.983 0.972 0.107 0.023 4 0.5 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 0051105 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 256923 Total vertex volume 252720 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 837 471 1538 2.323 0.586 0.143 0.052 16 1.4 BA1_exvivo 2063 1375 3289 2.194 0.508 0.106 0.020 17 1.7 BA2_exvivo 864 570 682 1.544 0.373 0.136 0.027 8 0.9 BA3a_exvivo 1377 948 1485 1.479 0.359 0.095 0.018 9 0.9 BA3b_exvivo 1994 1111 3391 2.740 0.659 0.107 0.032 19 2.8 BA4a_exvivo 1038 661 1469 2.325 0.563 0.108 0.027 8 1.1 BA4p_exvivo 5070 3270 11119 2.846 0.594 0.118 0.030 54 6.2 BA6_exvivo 1390 951 3367 2.811 0.591 0.134 0.030 20 1.9 BA44_exvivo 1214 813 2925 2.822 0.451 0.128 0.032 16 1.6 BA45_exvivo 3936 2695 4544 1.716 0.463 0.152 0.046 59 7.7 V1_exvivo 4345 2839 5858 1.875 0.533 0.172 0.057 87 10.0 V2_exvivo 479 344 1045 2.389 0.590 0.137 0.030 7 0.5 MT_exvivo 244 156 918 3.574 0.895 0.072 0.010 1 0.1 perirhinal_exvivo 266 184 717 3.115 0.896 0.089 0.024 2 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 01:51:56 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 21309 of (21309 21315 21321 21326 21333) to complete... Waiting for PID 21315 of (21309 21315 21321 21326 21333) to complete... Waiting for PID 21321 of (21309 21315 21321 21326 21333) to complete... Waiting for PID 21326 of (21309 21315 21321 21326 21333) to complete... Waiting for PID 21333 of (21309 21315 21321 21326 21333) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 406 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4368 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 561 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7248 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4092 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4789 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 457 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6204 mri_label2label: Done PIDs (21309 21315 21321 21326 21333) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 21388 of (21388 21394 21400 21406) to complete... Waiting for PID 21394 of (21388 21394 21400 21406) to complete... Waiting for PID 21400 of (21388 21394 21400 21406) to complete... Waiting for PID 21406 of (21388 21394 21400 21406) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4739 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 928 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13184 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 983 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7895 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 1341 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6696 mri_label2label: Done PIDs (21388 21394 21400 21406) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 21453 of (21453 21459 21465 21470 21476) to complete... Waiting for PID 21459 of (21453 21459 21465 21470 21476) to complete... Waiting for PID 21465 of (21453 21459 21465 21470 21476) to complete... Waiting for PID 21470 of (21453 21459 21465 21470 21476) to complete... Waiting for PID 21476 of (21453 21459 21465 21470 21476) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 1743 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6470 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 2704 Checking for and removing duplicates Writing label file ./rh.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/rh.MT_exvivo.label --trgsubject 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 584 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2516 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1116 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 825 mri_label2label: Done PIDs (21453 21459 21465 21470 21476) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 21526 of (21526 21532 21538 21548 21573) to complete... Waiting for PID 21532 of (21526 21532 21538 21548 21573) to complete... Waiting for PID 21538 of (21526 21532 21538 21548 21573) to complete... Waiting for PID 21548 of (21526 21532 21538 21548 21573) to complete... Waiting for PID 21573 of (21526 21532 21538 21548 21573) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 199 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2887 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1726 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2277 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1501 mri_label2label: Done PIDs (21526 21532 21538 21548 21573) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 21640 of (21640 21646 21652 21658) to complete... Waiting for PID 21646 of (21640 21646 21652 21658) to complete... Waiting for PID 21652 of (21640 21646 21652 21658) to complete... Waiting for PID 21658 of (21640 21646 21652 21658) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1594 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 448 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7407 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1161 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1388 mri_label2label: Done PIDs (21640 21646 21652 21658) 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 0051105 --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 0051105 --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 0051105 --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 0051105 --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 0051105 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 21720 of (21720 21726 21732 21738 21744) to complete... Waiting for PID 21726 of (21720 21726 21732 21738 21744) to complete... Waiting for PID 21732 of (21720 21726 21732 21738 21744) to complete... Waiting for PID 21738 of (21720 21726 21732 21738 21744) to complete... Waiting for PID 21744 of (21720 21726 21732 21738 21744) 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 1171 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4403 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 1423 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4860 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 335 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 741 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 0051105 --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 = 0051105 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-6.0.0/0051105/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 135698 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 317 mri_label2label: Done PIDs (21720 21726 21732 21738 21744) completed and logs appended. mris_label2annot --s 0051105 --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-6.0.0/0051105/label cmdline mris_label2annot --s 0051105 --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-967 machine x86_64 user ntraut subject 0051105 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-6.0.0/0051105/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 93499 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/label/rh.BA_exvivo.annot mris_label2annot --s 0051105 --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-6.0.0/0051105/label cmdline mris_label2annot --s 0051105 --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-967 machine x86_64 user ntraut subject 0051105 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-6.0.0/0051105/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 112163 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/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 0051105 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 253688 Total vertex volume 250027 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 1111 624 1976 2.304 0.554 0.148 0.045 20 1.8 BA1_exvivo 3662 2372 5411 2.229 0.496 0.106 0.025 30 3.5 BA2_exvivo 1026 670 893 1.755 0.361 0.145 0.035 12 1.3 BA3a_exvivo 1944 1325 2368 1.591 0.491 0.106 0.024 15 1.9 BA3b_exvivo 1653 951 3227 2.823 0.556 0.108 0.036 17 2.4 BA4a_exvivo 1223 786 1823 2.441 0.544 0.108 0.032 8 1.7 BA4p_exvivo 7809 5041 17613 2.913 0.583 0.114 0.031 78 9.6 BA6_exvivo 3647 2517 8037 2.834 0.593 0.114 0.024 35 3.6 BA44_exvivo 4762 3336 10471 2.655 0.586 0.139 0.037 74 6.7 BA45_exvivo 4079 2829 5404 1.817 0.517 0.163 0.052 69 8.6 V1_exvivo 8072 5329 12214 2.058 0.569 0.158 0.048 133 15.2 V2_exvivo 2315 1536 3542 2.210 0.463 0.137 0.033 33 3.1 MT_exvivo 539 401 1938 3.322 0.774 0.128 0.040 5 0.9 perirhinal_exvivo 357 252 1022 3.005 0.835 0.108 0.023 3 0.3 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 0051105 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051105/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 253688 Total vertex volume 250027 (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) = 1405286 mm^3 (det: 1.386270 ) lhCtxGM: 252281.745 251684.000 diff= 597.7 pctdiff= 0.237 rhCtxGM: 249143.146 248405.000 diff= 738.1 pctdiff= 0.296 lhCtxWM: 211113.416 211527.000 diff= -413.6 pctdiff=-0.196 rhCtxWM: 211287.381 211771.000 diff= -483.6 pctdiff=-0.229 SubCortGMVol 57913.000 SupraTentVol 992874.688 (990095.000) diff=2779.688 pctdiff=0.280 SupraTentVolNotVent 984157.688 (981378.000) diff=2779.688 pctdiff=0.282 BrainSegVol 1117087.000 (1115565.000) diff=1522.000 pctdiff=0.136 BrainSegVolNotVent 1106260.000 (1106552.688) diff=-292.688 pctdiff=-0.026 BrainSegVolNotVent 1106260.000 CerebellumVol 124736.000 VentChorVol 8717.000 3rd4th5thCSF 2110.000 CSFVol 588.000, OptChiasmVol 146.000 MaskVol 1488370.000 716 405 1125 2.056 0.559 0.151 0.049 15 1.4 BA1_exvivo 2052 1310 3106 2.201 0.485 0.100 0.024 15 1.9 BA2_exvivo 887 586 724 1.732 0.336 0.142 0.034 9 1.2 BA3a_exvivo 1496 1038 1561 1.431 0.323 0.096 0.020 9 1.2 BA3b_exvivo 968 565 1901 2.740 0.595 0.119 0.039 11 1.5 BA4a_exvivo 1089 681 1565 2.448 0.526 0.105 0.036 7 1.8 BA4p_exvivo 4990 3198 11339 2.944 0.603 0.114 0.032 51 6.4 BA6_exvivo 944 666 2350 2.909 0.541 0.119 0.026 11 1.2 BA44_exvivo 1118 804 2683 2.634 0.634 0.143 0.040 20 1.6 BA45_exvivo 3937 2699 4912 1.786 0.494 0.160 0.051 67 8.1 V1_exvivo 4474 2939 7076 2.070 0.592 0.170 0.056 85 9.8 V2_exvivo 303 205 635 2.338 0.462 0.154 0.037 6 0.5 MT_exvivo 311 223 1158 3.407 0.679 0.111 0.032 2 0.5 perirhinal_exvivo 250 185 512 2.683 0.527 0.124 0.030 2 0.2 entorhinal_exvivo Started at Sat Oct 7 17:43:51 CEST 2017 Ended at Sun Oct 8 01:54:58 CEST 2017 #@#%# recon-all-run-time-hours 8.185 recon-all -s 0051105 finished without error at Sun Oct 8 01:54:58 CEST 2017