Sat Oct 7 18:13:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050006 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050006 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-573 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: 65993848 59156296 6837552 1763032 0 54557664 -/+ buffers/cache: 4598632 61395216 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: 2017/10/07-16:13:09-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-573 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: 2017/10/07-16:13:09-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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: 2017/10/07-16:13:10-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-573 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-6.0.0/0050006 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Pitt/0050006/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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/Pitt/0050006/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-6.0.0/0050006/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 18:13:14 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 18:13:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-573 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 18:13:25 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.10258 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10258/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10258/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.10258/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 18:13:28 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10258/nu0.mnc ./tmp.mri_nu_correct.mni.10258/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10258/0/ -iterations 1000 -distance 50 [ntraut@tars-573:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/] [2017-10-07 18:13:28] 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.10258/0/ ./tmp.mri_nu_correct.mni.10258/nu0.mnc ./tmp.mri_nu_correct.mni.10258/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 61 CV of field change: 0.000983766 mri_convert ./tmp.mri_nu_correct.mni.10258/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.10258/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.10258/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 18:14:46 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 18:14:46 CEST 2017 Ended at Sat Oct 7 18:15:26 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 18:15:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7494, pval=0.6675 >= threshold=0.0050) awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach_avi.log TalAviQA: 0.97802 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 18:15:28 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-6.0.0/0050006/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-573 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 18:15:28 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.11283 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11283/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11283/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.11283/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 18:15:31 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.11283/nu0.mnc ./tmp.mri_nu_correct.mni.11283/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11283/0/ [ntraut@tars-573:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/] [2017-10-07 18:15:31] 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.11283/0/ ./tmp.mri_nu_correct.mni.11283/nu0.mnc ./tmp.mri_nu_correct.mni.11283/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00126908 -------------------------------------------------------- Iteration 2 Sat Oct 7 18:16:25 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.11283/nu1.mnc ./tmp.mri_nu_correct.mni.11283/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11283/1/ [ntraut@tars-573:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/] [2017-10-07 18:16:25] 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.11283/1/ ./tmp.mri_nu_correct.mni.11283/nu1.mnc ./tmp.mri_nu_correct.mni.11283/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00116069 mri_binarize --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11283/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-6.0.0/0050006/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11283/ones.mgz sysname Linux hostname tars-573 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.11283/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.11283/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.11283/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/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.11283/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/input.mean.dat sysname Linux hostname tars-573 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11283/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.11283/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11283/ones.mgz --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/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.11283/ones.mgz --i ./tmp.mri_nu_correct.mni.11283/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11283/output.mean.dat sysname Linux hostname tars-573 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11283/ones.mgz Loading ./tmp.mri_nu_correct.mni.11283/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.11283/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.11283/nu2.mnc ./tmp.mri_nu_correct.mni.11283/nu2.mnc mul .78921812247572847802 Saving result to './tmp.mri_nu_correct.mni.11283/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.11283/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.11283/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.11283/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 (10, 155) to ( 3, 110) Sat Oct 7 18:17:55 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 18:17:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 1.03938 -0.02663 -0.11947 -2.32802; 0.04816 0.97053 0.23096 -2.73907; 0.08222 -0.18301 1.13977 30.61087; 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 = 21 Starting OpenSpline(): npoints = 21 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 70 (70), valley at 50 (50) csf peak at 35, setting threshold to 58 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 70 (70), valley at 49 (49) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 51 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 18:19:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=5.0 skull bounding box = (48, 47, 18) --> (208, 238, 223) using (101, 111, 121) as brain centroid... mean wm in atlas = 108, using box (81,87,96) --> (120, 134,146) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 4.8 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.253 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.238317 @ (-9.091, -9.091, -9.091) max log p = -4.197597 @ (4.545, 13.636, -4.545) max log p = -4.131002 @ (6.818, -6.818, 6.818) max log p = -4.098882 @ (-1.136, 1.136, -1.136) max log p = -4.088455 @ (-0.568, 0.568, -0.568) max log p = -4.074969 @ (0.284, 0.284, 0.284) Found translation: (0.9, -0.3, -8.2): log p = -4.075 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.934, old_max_log_p =-4.075 (thresh=-4.1) 1.06580 -0.15927 -0.02372 10.70670; 0.14032 1.20979 0.18014 -69.03804; 0.00000 -0.11161 0.99651 8.07736; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.934, old_max_log_p =-3.934 (thresh=-3.9) 1.06580 -0.15927 -0.02372 10.70670; 0.14032 1.20979 0.18014 -69.03804; 0.00000 -0.11161 0.99651 8.07736; 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=-3.833, old_max_log_p =-3.934 (thresh=-3.9) 1.05132 -0.04320 0.06034 -8.04028; 0.03416 1.23318 0.23959 -62.22223; -0.07308 -0.18299 0.96223 29.65242; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.811, old_max_log_p =-3.833 (thresh=-3.8) 1.03196 -0.07433 0.01864 1.85345; 0.06734 1.24745 0.27801 -72.98422; -0.04166 -0.22705 0.97279 28.69073; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.801, old_max_log_p =-3.811 (thresh=-3.8) 1.03196 -0.07433 0.01864 1.85345; 0.06734 1.24745 0.27801 -72.98422; -0.04088 -0.22279 0.95455 30.23259; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.801, old_max_log_p =-3.801 (thresh=-3.8) 1.03196 -0.07433 0.01864 1.85345; 0.06734 1.24745 0.27801 -72.98422; -0.04088 -0.22279 0.95455 30.23259; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.788, old_max_log_p =-3.801 (thresh=-3.8) 1.03090 -0.05748 0.03876 -1.86785; 0.05046 1.24855 0.27742 -70.92123; -0.05789 -0.22206 0.95636 33.00936; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.787, old_max_log_p =-3.788 (thresh=-3.8) 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 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 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.787 (old=-4.253) transform before final EM align: 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 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 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 1.03134 -0.05566 0.03093 -1.69494; 0.05040 1.24709 0.27709 -70.67151; -0.04940 -0.22226 0.95552 32.06758; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1395.444860 mri_em_register stimesec 1.555763 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 157614 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 171 mri_em_register ru_nivcsw 2884 registration took 12 minutes and 2 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=126 y=116 z=119 r=74 first estimation of the main basin volume: 1713102 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=147, y=105, z=84, Imax=255 CSF=14, 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=9517038391 voxels, voxel volume =1.000 = 9517038391 mmm3 = 9517038.592 cm3 done. PostAnalyze...Basin Prior 63 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=127,y=123, z=111, r=10060 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=14, CSF_MAX=52 , nb = 42362 RIGHT_CER CSF_MIN=0, CSF_intensity=11, CSF_MAX=53 , nb = -1029149068 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=71 , nb = -1048385534 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=48 , nb = 1058576794 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=49 , nb = 1077599602 OTHER CSF_MIN=3, CSF_intensity=30, CSF_MAX=35 , nb = 1069764614 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 52, 51, 51, 67 after analyzing : 41, 51, 51, 55 RIGHT_CER before analyzing : 53, 49, 48, 69 after analyzing : 39, 49, 49, 54 LEFT_CER before analyzing : 71, 51, 45, 66 after analyzing : 38, 51, 51, 54 RIGHT_BRAIN before analyzing : 48, 49, 51, 67 after analyzing : 48, 50, 51, 54 LEFT_BRAIN before analyzing : 49, 50, 51, 67 after analyzing : 49, 50, 51, 54 OTHER before analyzing : 35, 33, 31, 40 after analyzing : 32, 33, 33, 34 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.136, std = 8.454 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.77, sigma = 2.84 after rotation: sse = 1.77, sigma = 2.84 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.83, its var is 2.36 before Erosion-Dilatation 0.01% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1704380 voxels, voxel volume = 1.000 mm3 = 1704380 mmm3 = 1704.380 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 29.383533 mri_watershed stimesec 0.523920 mri_watershed ru_maxrss 831296 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 215158 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 8808 mri_watershed ru_oublock 2680 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 2145 mri_watershed ru_nivcsw 113 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 18:32:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=29.9 skull bounding box = (61, 63, 30) --> (195, 183, 206) using (106, 103, 118) as brain centroid... mean wm in atlas = 107, using box (90,88,96) --> (122, 117,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 3.7 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -3.839 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.838664 @ (0.000, 0.000, 0.000) max log p = -3.806117 @ (-4.545, -4.545, -4.545) max log p = -3.624559 @ (2.273, 2.273, -2.273) max log p = -3.600117 @ (1.136, 1.136, -1.136) max log p = -3.600117 @ (0.000, 0.000, 0.000) max log p = -3.587332 @ (0.852, -0.852, -0.284) Found translation: (-0.3, -2.0, -8.2): log p = -3.587 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.485, old_max_log_p =-3.587 (thresh=-3.6) 1.00000 0.00000 0.00000 -0.28409; 0.00000 1.06580 0.14032 -25.92068; 0.00000 -0.13053 0.99144 8.56398; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.477, old_max_log_p =-3.485 (thresh=-3.5) 1.07500 0.00000 0.00000 -9.81069; 0.00000 1.14574 0.15084 -36.81149; 0.00000 -0.12074 0.91709 15.83001; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.477, old_max_log_p =-3.477 (thresh=-3.5) 1.07500 0.00000 0.00000 -9.81069; 0.00000 1.14574 0.15084 -36.81149; 0.00000 -0.12074 0.91709 15.83001; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.331, old_max_log_p =-3.477 (thresh=-3.5) 1.03026 -0.08375 0.04361 1.07080; 0.06884 1.11089 0.20991 -48.04515; -0.07294 -0.20231 0.93719 36.45243; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.331, old_max_log_p =-3.331 (thresh=-3.3) 1.03026 -0.08375 0.04361 1.07080; 0.06884 1.11089 0.20991 -48.04515; -0.07294 -0.20231 0.93719 36.45243; 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=-3.294, old_max_log_p =-3.331 (thresh=-3.3) 1.03130 -0.08073 0.02826 1.78981; 0.07019 1.11665 0.19507 -47.28871; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.292, old_max_log_p =-3.294 (thresh=-3.3) 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 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 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.292 (old=-3.839) transform before final EM align: 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 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 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.8 tol 0.000000 final transform: 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1091.679039 mri_em_register stimesec 1.400787 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 158957 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 85 mri_em_register ru_nivcsw 1811 registration took 9 minutes and 22 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 18:41:41 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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=29.9 skull bounding box = (61, 63, 30) --> (195, 183, 206) using (106, 103, 118) as brain centroid... mean wm in atlas = 107, using box (90,88,96) --> (122, 117,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 3.7 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.02888 -0.08054 0.02819 2.08266; 0.07035 1.11927 0.19553 -47.67913; -0.05470 -0.18472 0.93780 31.91876; 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 (127, 62, 30) --> (193, 163, 204) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 4958 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 65, 27) --> (128, 167, 203) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 4947 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 143, 59) --> (180, 179, 115) Left_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 144, 54) --> (131, 182, 115) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 17 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 131, 95) --> (148, 194, 127) Brain_Stem: limiting intensities to 91.0 --> 132.0 0 of 45 (0.0%) samples deleted using 9976 total control points for intensity normalization... bias field = 0.971 +- 0.037 51 of 9976 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 62, 30) --> (193, 163, 204) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 5587 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 65, 27) --> (128, 167, 203) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 5623 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 143, 59) --> (180, 179, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 62 (29.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 144, 54) --> (131, 182, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 59 (13.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 131, 95) --> (148, 194, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 11 of 132 (8.3%) samples deleted using 11463 total control points for intensity normalization... bias field = 1.039 +- 0.041 89 of 11316 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 62, 30) --> (193, 163, 204) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 2 of 5644 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 65, 27) --> (128, 167, 203) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 5 of 5557 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 143, 59) --> (180, 179, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 33 of 103 (32.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 144, 54) --> (131, 182, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 78 (6.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 131, 95) --> (148, 194, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 43 of 188 (22.9%) samples deleted using 11570 total control points for intensity normalization... bias field = 1.036 +- 0.039 89 of 11328 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 38 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 18:43:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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) = 1.12 (predicted orig area = 7.1) 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=0.767, neg=0, invalid=762 0001: dt=226.354978, rms=0.724 (5.666%), neg=0, invalid=762 0002: dt=161.113043, rms=0.712 (1.602%), neg=0, invalid=762 0003: dt=369.920000, rms=0.704 (1.164%), neg=0, invalid=762 0004: dt=136.533333, rms=0.700 (0.592%), neg=0, invalid=762 0005: dt=517.888000, rms=0.695 (0.623%), neg=0, invalid=762 0006: dt=129.472000, rms=0.693 (0.266%), neg=0, invalid=762 0007: dt=887.808000, rms=0.689 (0.553%), neg=0, invalid=762 0008: dt=110.976000, rms=0.688 (0.222%), neg=0, invalid=762 0009: dt=110.976000, rms=0.688 (0.054%), neg=0, invalid=762 0010: dt=110.976000, rms=0.687 (0.097%), neg=0, invalid=762 0011: dt=110.976000, rms=0.686 (0.136%), neg=0, invalid=762 0012: dt=110.976000, rms=0.685 (0.157%), neg=0, invalid=762 0013: dt=110.976000, rms=0.684 (0.181%), neg=0, invalid=762 0014: dt=110.976000, rms=0.682 (0.179%), neg=0, invalid=762 0015: dt=110.976000, rms=0.681 (0.169%), neg=0, invalid=762 0016: dt=110.976000, rms=0.680 (0.154%), neg=0, invalid=762 0017: dt=110.976000, rms=0.679 (0.139%), neg=0, invalid=762 0018: dt=110.976000, rms=0.679 (0.117%), neg=0, invalid=762 0019: dt=110.976000, rms=0.678 (0.112%), neg=0, invalid=762 0020: dt=2071.552000, rms=0.676 (0.235%), neg=0, invalid=762 0021: dt=110.976000, rms=0.676 (0.089%), neg=0, invalid=762 0022: dt=110.976000, rms=0.675 (0.017%), neg=0, invalid=762 0023: dt=110.976000, rms=0.675 (0.025%), neg=0, invalid=762 0024: dt=110.976000, rms=0.675 (0.035%), neg=0, invalid=762 0025: dt=110.976000, rms=0.675 (0.056%), neg=0, invalid=762 0026: dt=110.976000, rms=0.674 (0.050%), neg=0, invalid=762 0027: dt=110.976000, rms=0.674 (0.056%), neg=0, invalid=762 0028: dt=110.976000, rms=0.674 (0.053%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.674, neg=0, invalid=762 0029: dt=221.952000, rms=0.672 (0.304%), neg=0, invalid=762 0030: dt=443.904000, rms=0.671 (0.102%), neg=0, invalid=762 0031: dt=443.904000, rms=0.671 (0.043%), neg=0, invalid=762 0032: dt=443.904000, rms=0.670 (0.188%), neg=0, invalid=762 0033: dt=443.904000, rms=0.669 (0.092%), neg=0, invalid=762 0034: dt=443.904000, rms=0.668 (0.162%), neg=0, invalid=762 0035: dt=443.904000, rms=0.667 (0.138%), neg=0, invalid=762 0036: dt=443.904000, rms=0.666 (0.110%), neg=0, invalid=762 0037: dt=443.904000, rms=0.665 (0.159%), neg=0, invalid=762 0038: dt=443.904000, rms=0.664 (0.171%), neg=0, invalid=762 0039: dt=443.904000, rms=0.663 (0.123%), neg=0, invalid=762 0040: dt=443.904000, rms=0.662 (0.156%), neg=0, invalid=762 0041: dt=443.904000, rms=0.662 (0.129%), neg=0, invalid=762 0042: dt=443.904000, rms=0.661 (0.093%), neg=0, invalid=762 0043: dt=443.904000, rms=0.660 (0.142%), neg=0, invalid=762 0044: dt=443.904000, rms=0.659 (0.126%), neg=0, invalid=762 0045: dt=443.904000, rms=0.658 (0.110%), neg=0, invalid=762 0046: dt=443.904000, rms=0.658 (0.077%), neg=0, invalid=762 0047: dt=129.472000, rms=0.658 (0.042%), neg=0, invalid=762 0048: dt=129.472000, rms=0.658 (0.001%), neg=0, invalid=762 0049: dt=129.472000, rms=0.658 (0.004%), neg=0, invalid=762 0050: dt=129.472000, rms=0.658 (0.005%), neg=0, invalid=762 0051: dt=129.472000, rms=0.658 (0.009%), neg=0, invalid=762 0052: dt=129.472000, rms=0.657 (0.009%), neg=0, invalid=762 0053: dt=129.472000, rms=0.657 (0.013%), neg=0, invalid=762 0054: dt=129.472000, rms=0.657 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0055: dt=78.278215, rms=0.660 (0.416%), neg=0, invalid=762 0056: dt=331.776000, rms=0.652 (1.235%), neg=0, invalid=762 0057: dt=62.608696, rms=0.650 (0.327%), neg=0, invalid=762 0058: dt=331.776000, rms=0.643 (1.009%), neg=0, invalid=762 0059: dt=44.444444, rms=0.640 (0.540%), neg=0, invalid=762 0060: dt=82.944000, rms=0.639 (0.048%), neg=0, invalid=762 0061: dt=82.944000, rms=0.638 (0.186%), neg=0, invalid=762 0062: dt=82.944000, rms=0.637 (0.251%), neg=0, invalid=762 0063: dt=82.944000, rms=0.635 (0.329%), neg=0, invalid=762 0064: dt=82.944000, rms=0.632 (0.470%), neg=0, invalid=762 0065: dt=82.944000, rms=0.628 (0.526%), neg=0, invalid=762 0066: dt=82.944000, rms=0.625 (0.441%), neg=0, invalid=762 0067: dt=82.944000, rms=0.623 (0.351%), neg=0, invalid=762 0068: dt=82.944000, rms=0.621 (0.390%), neg=0, invalid=762 0069: dt=82.944000, rms=0.619 (0.335%), neg=0, invalid=762 0070: dt=82.944000, rms=0.617 (0.211%), neg=0, invalid=762 0071: dt=82.944000, rms=0.616 (0.211%), neg=0, invalid=762 0072: dt=82.944000, rms=0.615 (0.227%), neg=0, invalid=762 0073: dt=82.944000, rms=0.614 (0.155%), neg=0, invalid=762 0074: dt=82.944000, rms=0.613 (0.136%), neg=0, invalid=762 0075: dt=82.944000, rms=0.612 (0.141%), neg=0, invalid=762 0076: dt=82.944000, rms=0.611 (0.114%), neg=0, invalid=762 0077: dt=82.944000, rms=0.611 (0.093%), neg=0, invalid=762 0078: dt=145.152000, rms=0.610 (0.062%), neg=0, invalid=762 0079: dt=145.152000, rms=0.610 (-0.250%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=762 0080: dt=64.226148, rms=0.609 (0.334%), neg=0, invalid=762 0081: dt=124.416000, rms=0.609 (0.109%), neg=0, invalid=762 0082: dt=124.416000, rms=0.608 (0.070%), neg=0, invalid=762 0083: dt=124.416000, rms=0.607 (0.116%), neg=0, invalid=762 0084: dt=124.416000, rms=0.607 (-0.075%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0085: dt=9.600000, rms=0.632 (0.230%), neg=0, invalid=762 0086: dt=2.800000, rms=0.631 (0.013%), neg=0, invalid=762 0087: dt=2.800000, rms=0.631 (0.006%), neg=0, invalid=762 0088: dt=2.800000, rms=0.631 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.632, neg=0, invalid=762 0089: dt=1.600000, rms=0.631 (0.112%), neg=0, invalid=762 0090: dt=0.500000, rms=0.631 (-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=0.691, neg=0, invalid=762 0091: dt=5.864407, rms=0.671 (2.915%), neg=0, invalid=762 0092: dt=5.025641, rms=0.669 (0.279%), neg=0, invalid=762 0093: dt=2.304000, rms=0.669 (0.017%), neg=0, invalid=762 0094: dt=2.304000, rms=0.669 (0.002%), neg=0, invalid=762 0095: dt=2.304000, rms=0.669 (-0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0096: dt=0.000000, rms=0.669 (0.084%), neg=0, invalid=762 0097: dt=0.000000, rms=0.669 (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=0.708, neg=0, invalid=762 0098: dt=0.020000, rms=0.707 (0.076%), neg=0, invalid=762 0099: dt=0.007000, rms=0.707 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.708, neg=0, invalid=762 0100: dt=0.320000, rms=0.707 (0.108%), neg=0, invalid=762 0101: dt=0.256000, rms=0.707 (0.014%), neg=0, invalid=762 0102: dt=0.256000, rms=0.707 (0.009%), neg=0, invalid=762 0103: dt=0.256000, rms=0.707 (-0.018%), 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=0.653, neg=0, invalid=762 0104: dt=0.693878, rms=0.640 (2.037%), neg=0, invalid=762 0105: dt=0.064000, rms=0.639 (0.074%), neg=0, invalid=762 0106: dt=0.064000, rms=0.639 (-0.063%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=762 0107: dt=0.028000, rms=0.639 (0.108%), neg=0, invalid=762 0108: dt=0.004000, rms=0.639 (0.001%), neg=0, invalid=762 0109: dt=0.004000, rms=0.639 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.09740 (22) Left_Lateral_Ventricle (4): linear fit = 1.22 x + 0.0 (723 voxels, overlap=0.468) Left_Lateral_Ventricle (4): linear fit = 1.22 x + 0.0 (723 voxels, peak = 24), gca=24.3 gca peak = 0.15565 (16) mri peak = 0.08725 (22) Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (983 voxels, overlap=0.414) Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (983 voxels, peak = 21), gca=21.4 gca peak = 0.26829 (96) mri peak = 0.09091 (91) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1016 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1016 voxels, peak = 92), gca=91.7 gca peak = 0.20183 (93) mri peak = 0.07473 (94) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (909 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (909 voxels, peak = 91), gca=90.7 gca peak = 0.21683 (55) mri peak = 0.10283 (64) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (903 voxels, overlap=0.223) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (903 voxels, peak = 62), gca=62.4 gca peak = 0.30730 (58) mri peak = 0.09265 (66) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1017 voxels, overlap=0.588) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1017 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.12476 (103) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68436 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68436 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.12561 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (69742 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (69742 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.04342 (66) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (35342 voxels, overlap=0.566) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (35342 voxels, peak = 68), gca=67.6 gca peak = 0.15082 (58) mri peak = 0.04774 (67) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (36742 voxels, overlap=0.536) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (36742 voxels, peak = 65), gca=64.7 gca peak = 0.14161 (67) mri peak = 0.10644 (75) Right_Caudate (50): linear fit = 1.09 x + 0.0 (905 voxels, overlap=0.562) Right_Caudate (50): linear fit = 1.09 x + 0.0 (905 voxels, peak = 73), gca=72.7 gca peak = 0.15243 (71) mri peak = 0.12975 (79) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1122 voxels, overlap=0.650) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1122 voxels, peak = 76), gca=75.6 gca peak = 0.13336 (57) mri peak = 0.04221 (61) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (36388 voxels, overlap=0.936) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (36388 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.04284 (59) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35269 voxels, overlap=0.944) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35269 voxels, peak = 60), gca=59.6 gca peak = 0.18181 (84) mri peak = 0.03868 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9481 voxels, overlap=0.517) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9481 voxels, peak = 94), gca=93.7 gca peak = 0.20573 (83) mri peak = 0.04901 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8017 voxels, overlap=0.458) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8017 voxels, peak = 93), gca=92.5 gca peak = 0.21969 (57) mri peak = 0.09678 (67) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (486 voxels, overlap=0.288) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (486 voxels, peak = 65), gca=64.7 gca peak = 0.39313 (56) mri peak = 0.08696 (67) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (574 voxels, overlap=0.152) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (574 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.06497 (87) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5916 voxels, overlap=0.960) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5916 voxels, peak = 86), gca=86.3 gca peak = 0.11978 (83) mri peak = 0.06782 (84) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5139 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5139 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.07183 (82) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2685 voxels, overlap=0.865) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2685 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.08491 (81) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2744 voxels, overlap=0.912) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2744 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.07592 (93) Brain_Stem (16): linear fit = 1.15 x + 0.0 (11293 voxels, overlap=0.108) Brain_Stem (16): linear fit = 1.15 x + 0.0 (11293 voxels, peak = 92), gca=92.4 gca peak = 0.13281 (86) mri peak = 0.06537 (91) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1349 voxels, overlap=0.631) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1349 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.07649 (91) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1636 voxels, overlap=0.752) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1636 voxels, peak = 93), gca=93.0 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.08814 (21) Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (393 voxels, overlap=0.804) Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (393 voxels, peak = 20), gca=20.3 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 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 1.13 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.17 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=0.633, neg=0, invalid=762 0110: dt=129.472000, rms=0.626 (1.057%), neg=0, invalid=762 0111: dt=221.952000, rms=0.624 (0.359%), neg=0, invalid=762 0112: dt=295.936000, rms=0.622 (0.314%), neg=0, invalid=762 0113: dt=129.472000, rms=0.621 (0.116%), neg=0, invalid=762 0114: dt=517.888000, rms=0.619 (0.254%), neg=0, invalid=762 0115: dt=73.984000, rms=0.619 (0.080%), neg=0, invalid=762 0116: dt=443.904000, rms=0.618 (0.095%), neg=0, invalid=762 0117: dt=129.472000, rms=0.618 (0.116%), neg=0, invalid=762 0118: dt=129.472000, rms=0.618 (0.021%), neg=0, invalid=762 0119: dt=129.472000, rms=0.617 (0.051%), neg=0, invalid=762 0120: dt=129.472000, rms=0.617 (0.068%), neg=0, invalid=762 0121: dt=129.472000, rms=0.616 (0.077%), neg=0, invalid=762 0122: dt=129.472000, rms=0.616 (0.103%), neg=0, invalid=762 0123: dt=129.472000, rms=0.615 (0.119%), neg=0, invalid=762 0124: dt=129.472000, rms=0.614 (0.115%), neg=0, invalid=762 0125: dt=129.472000, rms=0.614 (0.108%), neg=0, invalid=762 0126: dt=129.472000, rms=0.613 (0.108%), neg=0, invalid=762 0127: dt=129.472000, rms=0.612 (0.096%), neg=0, invalid=762 0128: dt=129.472000, rms=0.612 (0.096%), neg=0, invalid=762 0129: dt=129.472000, rms=0.611 (0.088%), neg=0, invalid=762 0130: dt=129.472000, rms=0.611 (0.079%), neg=0, invalid=762 0131: dt=129.472000, rms=0.610 (0.086%), neg=0, invalid=762 0132: dt=129.472000, rms=0.610 (0.087%), neg=0, invalid=762 0133: dt=129.472000, rms=0.609 (0.079%), neg=0, invalid=762 0134: dt=129.472000, rms=0.609 (0.050%), neg=0, invalid=762 0135: dt=129.472000, rms=0.609 (0.060%), neg=0, invalid=762 0136: dt=129.472000, rms=0.608 (0.072%), neg=0, invalid=762 0137: dt=129.472000, rms=0.608 (0.057%), neg=0, invalid=762 0138: dt=129.472000, rms=0.608 (0.034%), neg=0, invalid=762 0139: dt=129.472000, rms=0.607 (0.046%), neg=0, invalid=762 0140: dt=129.472000, rms=0.607 (0.058%), neg=0, invalid=762 0141: dt=129.472000, rms=0.607 (0.059%), neg=0, invalid=762 0142: dt=129.472000, rms=0.606 (0.042%), neg=0, invalid=762 0143: dt=129.472000, rms=0.606 (0.044%), neg=0, invalid=762 0144: dt=129.472000, rms=0.606 (0.048%), neg=0, invalid=762 0145: dt=129.472000, rms=0.605 (0.055%), neg=0, invalid=762 0146: dt=129.472000, rms=0.605 (0.051%), neg=0, invalid=762 0147: dt=129.472000, rms=0.605 (0.043%), neg=0, invalid=762 0148: dt=129.472000, rms=0.605 (0.041%), neg=0, invalid=762 0149: dt=129.472000, rms=0.604 (0.043%), neg=0, invalid=762 0150: dt=129.472000, rms=0.604 (0.035%), neg=0, invalid=762 0151: dt=129.472000, rms=0.604 (0.043%), neg=0, invalid=762 0152: dt=129.472000, rms=0.604 (0.028%), neg=0, invalid=762 0153: dt=129.472000, rms=0.603 (0.031%), neg=0, invalid=762 0154: dt=129.472000, rms=0.603 (0.039%), neg=0, invalid=762 0155: dt=129.472000, rms=0.603 (0.041%), neg=0, invalid=762 0156: dt=129.472000, rms=0.603 (0.029%), neg=0, invalid=762 0157: dt=129.472000, rms=0.603 (0.016%), neg=0, invalid=762 0158: dt=129.472000, rms=0.603 (0.029%), neg=0, invalid=762 0159: dt=129.472000, rms=0.602 (0.040%), neg=0, invalid=762 0160: dt=129.472000, rms=0.602 (0.038%), neg=0, invalid=762 0161: dt=129.472000, rms=0.602 (0.021%), neg=0, invalid=762 0162: dt=129.472000, rms=0.602 (0.017%), neg=0, invalid=762 0163: dt=1479.680000, rms=0.602 (0.053%), neg=0, invalid=762 0164: dt=8.092000, rms=0.602 (0.002%), neg=0, invalid=762 0165: dt=8.092000, rms=0.602 (0.000%), neg=0, invalid=762 0166: dt=8.092000, rms=0.602 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0167: dt=129.472000, rms=0.601 (0.173%), neg=0, invalid=762 0168: dt=443.904000, rms=0.600 (0.093%), neg=0, invalid=762 0169: dt=129.472000, rms=0.600 (0.029%), neg=0, invalid=762 0170: dt=129.472000, rms=0.600 (0.015%), neg=0, invalid=762 0171: dt=129.472000, rms=0.600 (0.027%), neg=0, invalid=762 0172: dt=129.472000, rms=0.600 (0.032%), neg=0, invalid=762 0173: dt=129.472000, rms=0.599 (0.034%), neg=0, invalid=762 0174: dt=129.472000, rms=0.599 (0.029%), neg=0, invalid=762 0175: dt=129.472000, rms=0.599 (0.030%), neg=0, invalid=762 0176: dt=129.472000, rms=0.599 (0.035%), neg=0, invalid=762 0177: dt=129.472000, rms=0.599 (0.029%), neg=0, invalid=762 0178: dt=129.472000, rms=0.599 (0.032%), neg=0, invalid=762 0179: dt=129.472000, rms=0.598 (0.026%), neg=0, invalid=762 0180: dt=129.472000, rms=0.598 (0.026%), neg=0, invalid=762 0181: dt=129.472000, rms=0.598 (0.027%), neg=0, invalid=762 0182: dt=129.472000, rms=0.598 (0.021%), neg=0, invalid=762 0183: dt=129.472000, rms=0.598 (0.022%), neg=0, invalid=762 0184: dt=129.472000, rms=0.598 (0.020%), neg=0, invalid=762 0185: dt=517.888000, rms=0.598 (0.013%), neg=0, invalid=762 0186: dt=517.888000, rms=0.598 (-0.116%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=762 0187: dt=36.288000, rms=0.597 (0.284%), neg=0, invalid=762 0188: dt=145.152000, rms=0.595 (0.357%), neg=0, invalid=762 0189: dt=145.152000, rms=0.589 (0.950%), neg=0, invalid=762 0190: dt=36.288000, rms=0.589 (0.067%), neg=0, invalid=762 0191: dt=248.832000, rms=0.587 (0.303%), neg=0, invalid=762 0192: dt=111.659574, rms=0.583 (0.769%), neg=0, invalid=762 0193: dt=25.920000, rms=0.582 (0.072%), neg=0, invalid=762 0194: dt=25.920000, rms=0.582 (0.017%), neg=0, invalid=762 0195: dt=25.920000, rms=0.582 (0.031%), neg=0, invalid=762 0196: dt=25.920000, rms=0.582 (0.057%), neg=0, invalid=762 0197: dt=25.920000, rms=0.581 (0.107%), neg=0, invalid=762 0198: dt=25.920000, rms=0.580 (0.170%), neg=0, invalid=762 0199: dt=25.920000, rms=0.579 (0.228%), neg=0, invalid=762 0200: dt=25.920000, rms=0.577 (0.258%), neg=0, invalid=762 0201: dt=25.920000, rms=0.577 (0.038%), neg=0, invalid=762 0202: dt=25.920000, rms=0.577 (0.070%), neg=0, invalid=762 0203: dt=25.920000, rms=0.576 (0.100%), neg=0, invalid=762 0204: dt=25.920000, rms=0.576 (0.041%), neg=0, invalid=762 0205: dt=25.920000, rms=0.576 (0.041%), neg=0, invalid=762 0206: dt=0.810000, rms=0.576 (0.002%), neg=0, invalid=762 0207: dt=0.202500, rms=0.576 (0.000%), neg=0, invalid=762 0208: dt=0.035437, rms=0.576 (0.000%), neg=0, invalid=762 0209: dt=0.035437, rms=0.576 (0.000%), neg=0, invalid=762 0210: dt=0.004430, rms=0.576 (0.000%), neg=0, invalid=762 0211: dt=0.002215, rms=0.576 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.576, neg=0, invalid=762 0212: dt=0.007594, rms=0.576 (0.086%), neg=0, invalid=762 0213: dt=0.000000, rms=0.576 (0.000%), neg=0, invalid=762 0214: dt=0.000439, rms=0.576 (0.000%), neg=0, invalid=762 0215: dt=0.000220, rms=0.576 (0.000%), neg=0, invalid=762 0216: dt=0.000110, rms=0.576 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.580, neg=0, invalid=762 0217: dt=0.000000, rms=0.580 (0.085%), neg=0, invalid=762 0218: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762 0219: dt=0.000002, rms=0.580 (0.000%), neg=0, invalid=762 0220: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762 0221: dt=0.000000, rms=0.580 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.580, neg=0, invalid=762 0222: dt=63.599284, rms=0.564 (2.775%), neg=0, invalid=762 0223: dt=25.600000, rms=0.555 (1.605%), neg=0, invalid=762 0224: dt=38.400000, rms=0.550 (0.831%), neg=0, invalid=762 0225: dt=25.253561, rms=0.547 (0.679%), neg=0, invalid=762 0226: dt=32.000000, rms=0.544 (0.544%), neg=0, invalid=762 0227: dt=25.600000, rms=0.541 (0.455%), neg=0, invalid=762 0228: dt=30.400000, rms=0.539 (0.420%), neg=0, invalid=762 0229: dt=25.500000, rms=0.537 (0.354%), neg=0, invalid=762 0230: dt=29.765079, rms=0.535 (0.344%), neg=0, invalid=762 0231: dt=25.339367, rms=0.534 (0.287%), neg=0, invalid=762 0232: dt=25.600000, rms=0.532 (0.286%), neg=0, invalid=762 0233: dt=32.000000, rms=0.531 (0.227%), neg=0, invalid=762 0234: dt=24.749245, rms=0.530 (0.255%), neg=0, invalid=762 0235: dt=25.600000, rms=0.529 (0.193%), neg=0, invalid=762 0236: dt=32.000000, rms=0.527 (0.203%), neg=0, invalid=762 0237: dt=24.236686, rms=0.527 (0.179%), neg=0, invalid=762 0238: dt=25.600000, rms=0.526 (0.167%), neg=0, invalid=762 0239: dt=32.000000, rms=0.525 (0.159%), neg=0, invalid=762 0240: dt=25.600000, rms=0.524 (0.148%), neg=0, invalid=762 0241: dt=25.600000, rms=0.523 (0.137%), neg=0, invalid=762 0242: dt=25.600000, rms=0.523 (0.121%), neg=0, invalid=762 0243: dt=38.400000, rms=0.522 (0.140%), neg=0, invalid=762 0244: dt=19.200000, rms=0.521 (0.124%), neg=0, invalid=762 0245: dt=44.800000, rms=0.520 (0.151%), neg=0, invalid=762 0246: dt=25.430464, rms=0.520 (0.107%), neg=0, invalid=762 0247: dt=25.600000, rms=0.519 (0.096%), neg=0, invalid=762 0248: dt=25.600000, rms=0.519 (0.091%), neg=0, invalid=762 0249: dt=32.000000, rms=0.518 (0.095%), neg=0, invalid=762 0250: dt=25.600000, rms=0.518 (0.084%), neg=0, invalid=762 0251: dt=32.000000, rms=0.518 (0.088%), neg=0, invalid=762 0252: dt=19.200000, rms=0.517 (0.078%), neg=0, invalid=762 0253: dt=44.800000, rms=0.517 (0.112%), neg=0, invalid=762 0254: dt=25.600000, rms=0.516 (0.069%), neg=0, invalid=762 0255: dt=32.000000, rms=0.516 (0.075%), neg=0, invalid=762 0256: dt=19.200000, rms=0.516 (0.068%), neg=0, invalid=762 0257: dt=44.800000, rms=0.515 (0.091%), neg=0, invalid=762 0258: dt=19.200000, rms=0.515 (0.058%), neg=0, invalid=762 0259: dt=44.800000, rms=0.514 (0.071%), neg=0, invalid=762 0260: dt=25.600000, rms=0.514 (0.067%), neg=0, invalid=762 0261: dt=32.000000, rms=0.514 (0.060%), neg=0, invalid=762 0262: dt=25.600000, rms=0.513 (0.052%), neg=0, invalid=762 0263: dt=32.000000, rms=0.513 (0.055%), neg=0, invalid=762 0264: dt=19.200000, rms=0.513 (0.053%), neg=0, invalid=762 0265: dt=44.800000, rms=0.513 (0.069%), neg=0, invalid=762 0266: dt=25.600000, rms=0.512 (0.047%), neg=0, invalid=762 0267: dt=25.600000, rms=0.512 (0.049%), neg=0, invalid=762 0268: dt=25.600000, rms=0.512 (0.077%), neg=0, invalid=762 0269: dt=25.600000, rms=0.511 (0.110%), neg=0, invalid=762 0270: dt=25.600000, rms=0.510 (0.130%), neg=0, invalid=762 0271: dt=25.600000, rms=0.510 (0.162%), neg=0, invalid=762 0272: dt=25.600000, rms=0.509 (0.159%), neg=0, invalid=762 0273: dt=25.600000, rms=0.508 (0.177%), neg=0, invalid=762 0274: dt=25.600000, rms=0.507 (0.172%), neg=0, invalid=762 0275: dt=25.600000, rms=0.506 (0.183%), neg=0, invalid=762 0276: dt=25.600000, rms=0.506 (0.015%), neg=0, invalid=762 0277: dt=25.600000, rms=0.506 (0.023%), neg=0, invalid=762 0278: dt=25.600000, rms=0.506 (0.051%), neg=0, invalid=762 0279: dt=25.600000, rms=0.505 (0.051%), neg=0, invalid=762 0280: dt=25.600000, rms=0.505 (0.006%), neg=0, invalid=762 0281: dt=25.600000, rms=0.505 (0.031%), neg=0, invalid=762 0282: dt=25.600000, rms=0.505 (0.052%), neg=0, invalid=762 0283: dt=25.600000, rms=0.505 (0.054%), neg=0, invalid=762 0284: dt=25.600000, rms=0.504 (0.058%), neg=0, invalid=762 0285: dt=25.600000, rms=0.504 (0.064%), neg=0, invalid=762 0286: dt=25.600000, rms=0.504 (0.083%), neg=0, invalid=762 0287: dt=6.400000, rms=0.504 (0.006%), neg=0, invalid=762 0288: dt=6.400000, rms=0.504 (0.004%), neg=0, invalid=762 0289: dt=11.200000, rms=0.504 (0.007%), neg=0, invalid=762 0290: dt=11.200000, rms=0.504 (0.002%), neg=0, invalid=762 0291: dt=11.200000, rms=0.504 (0.006%), neg=0, invalid=762 0292: dt=11.200000, rms=0.503 (0.010%), neg=0, invalid=762 0293: dt=11.200000, rms=0.503 (0.016%), neg=0, invalid=762 0294: dt=11.200000, rms=0.503 (0.016%), neg=0, invalid=762 0295: dt=11.200000, rms=0.503 (0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.520, neg=0, invalid=762 0296: dt=0.000000, rms=0.520 (0.086%), neg=0, invalid=762 0297: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=762 0298: dt=0.150000, rms=0.520 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=762 0299: dt=0.000000, rms=0.520 (0.086%), neg=0, invalid=762 0300: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=762 0301: dt=0.150000, rms=0.520 (-0.011%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0302: dt=1.280000, rms=0.550 (0.564%), neg=0, invalid=762 0303: dt=0.448000, rms=0.550 (0.024%), neg=0, invalid=762 0304: dt=0.448000, rms=0.550 (-0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.550, neg=0, invalid=762 0305: dt=1.024000, rms=0.549 (0.190%), neg=0, invalid=762 0306: dt=0.256000, rms=0.549 (0.005%), neg=0, invalid=762 0307: dt=0.256000, rms=0.549 (-0.002%), 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=0.515, neg=0, invalid=762 0308: dt=0.448000, rms=0.503 (2.313%), neg=0, invalid=762 0309: dt=0.448000, rms=0.500 (0.550%), neg=0, invalid=762 0310: dt=0.448000, rms=0.498 (0.305%), neg=0, invalid=762 0311: dt=0.448000, rms=0.498 (0.178%), neg=0, invalid=762 0312: dt=0.448000, rms=0.497 (0.129%), neg=0, invalid=762 0313: dt=0.448000, rms=0.496 (0.088%), neg=0, invalid=762 0314: dt=0.448000, rms=0.496 (0.076%), neg=0, invalid=762 0315: dt=0.448000, rms=0.496 (0.053%), neg=0, invalid=762 0316: dt=0.448000, rms=0.496 (0.047%), neg=0, invalid=762 0317: dt=0.448000, rms=0.495 (0.032%), neg=0, invalid=762 0318: dt=0.448000, rms=0.495 (0.059%), neg=0, invalid=762 0319: dt=0.448000, rms=0.495 (0.078%), neg=0, invalid=762 0320: dt=0.448000, rms=0.494 (0.070%), neg=0, invalid=762 0321: dt=0.448000, rms=0.494 (0.048%), neg=0, invalid=762 0322: dt=0.448000, rms=0.494 (0.037%), neg=0, invalid=762 0323: dt=0.448000, rms=0.494 (0.018%), neg=0, invalid=762 0324: dt=0.448000, rms=0.494 (-0.003%), neg=0, invalid=762 0325: dt=0.028000, rms=0.494 (0.000%), neg=0, invalid=762 0326: dt=0.000750, rms=0.494 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.494, neg=0, invalid=762 0327: dt=0.448000, rms=0.490 (0.957%), neg=0, invalid=762 0328: dt=0.448000, rms=0.489 (0.154%), neg=0, invalid=762 0329: dt=0.448000, rms=0.489 (0.043%), neg=0, invalid=762 0330: dt=0.448000, rms=0.489 (0.025%), neg=0, invalid=762 0331: dt=0.448000, rms=0.488 (0.015%), neg=0, invalid=762 0332: dt=0.224000, rms=0.488 (-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=0.487, neg=0, invalid=762 0333: dt=0.000000, rms=0.486 (0.103%), neg=0, invalid=762 0334: dt=0.000000, rms=0.486 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=762 0335: dt=129.472000, rms=0.486 (0.140%), neg=0, invalid=762 0336: dt=110.976000, rms=0.486 (0.008%), neg=0, invalid=762 0337: dt=110.976000, rms=0.486 (0.020%), neg=0, invalid=762 0338: dt=110.976000, rms=0.486 (0.011%), neg=0, invalid=762 0339: dt=110.976000, rms=0.486 (0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.486, neg=0, invalid=762 0340: dt=9.072000, rms=0.486 (0.111%), neg=0, invalid=762 0341: dt=1.620000, rms=0.486 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=762 0342: dt=145.152000, rms=0.484 (0.386%), neg=0, invalid=762 0343: dt=31.104000, rms=0.484 (0.095%), neg=0, invalid=762 0344: dt=31.104000, rms=0.484 (0.039%), neg=0, invalid=762 0345: dt=31.104000, rms=0.483 (0.062%), neg=0, invalid=762 0346: dt=31.104000, rms=0.483 (0.079%), neg=0, invalid=762 0347: dt=31.104000, rms=0.483 (0.084%), neg=0, invalid=762 0348: dt=31.104000, rms=0.482 (0.087%), neg=0, invalid=762 0349: dt=31.104000, rms=0.482 (0.087%), neg=0, invalid=762 0350: dt=31.104000, rms=0.481 (0.074%), neg=0, invalid=762 0351: dt=248.832000, rms=0.481 (0.054%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0352: dt=11.200000, rms=0.481 (0.292%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=0, neg = 0 0353: dt=24.483221, rms=0.480 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0354: dt=24.483221, rms=0.479 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 3 iterations, nbhd size=0, neg = 0 0355: dt=24.483221, rms=0.478 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 11 iterations, nbhd size=1, neg = 0 0356: dt=24.483221, rms=0.478 (0.024%), neg=0, invalid=762 iter 0, gcam->neg = 43 after 8 iterations, nbhd size=0, neg = 0 0357: dt=24.483221, rms=0.478 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 14 iterations, nbhd size=1, neg = 0 0358: dt=24.483221, rms=0.478 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 61 after 17 iterations, nbhd size=1, neg = 0 0359: dt=24.483221, rms=0.477 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 49 after 17 iterations, nbhd size=1, neg = 0 0360: dt=24.483221, rms=0.476 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 41 after 16 iterations, nbhd size=1, neg = 0 0361: dt=24.483221, rms=0.475 (0.213%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 13 iterations, nbhd size=1, neg = 0 0362: dt=24.483221, rms=0.474 (0.237%), neg=0, invalid=762 iter 0, gcam->neg = 37 after 13 iterations, nbhd size=1, neg = 0 0363: dt=24.483221, rms=0.473 (0.189%), neg=0, invalid=762 iter 0, gcam->neg = 39 after 15 iterations, nbhd size=1, neg = 0 0364: dt=24.483221, rms=0.472 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 38 after 5 iterations, nbhd size=0, neg = 0 0365: dt=24.483221, rms=0.471 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 13 iterations, nbhd size=1, neg = 0 0366: dt=24.483221, rms=0.471 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 45 after 7 iterations, nbhd size=0, neg = 0 0367: dt=24.483221, rms=0.470 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0368: dt=44.800000, rms=0.470 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0369: dt=32.000000, rms=0.469 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 11 iterations, nbhd size=1, neg = 0 0370: dt=32.000000, rms=0.469 (0.019%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0371: dt=32.000000, rms=0.469 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0372: dt=32.000000, rms=0.469 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0373: dt=32.000000, rms=0.468 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 8 iterations, nbhd size=0, neg = 0 0374: dt=32.000000, rms=0.468 (-0.021%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0375: dt=38.400000, rms=0.465 (0.869%), neg=0, invalid=762 0376: dt=25.600000, rms=0.463 (0.285%), neg=0, invalid=762 0377: dt=32.000000, rms=0.462 (0.217%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0378: dt=32.000000, rms=0.462 (0.090%), neg=0, invalid=762 0379: dt=32.000000, rms=0.461 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0380: dt=32.000000, rms=0.460 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0381: dt=32.000000, rms=0.459 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0382: dt=32.000000, rms=0.459 (0.016%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0383: dt=32.000000, rms=0.459 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0384: dt=32.000000, rms=0.459 (-0.018%), neg=0, invalid=762 0385: dt=38.400000, rms=0.458 (0.095%), neg=0, invalid=762 0386: dt=25.600000, rms=0.458 (0.063%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0387: dt=1.333333, rms=0.464 (0.109%), neg=0, invalid=762 0388: dt=0.576000, rms=0.464 (0.005%), neg=0, invalid=762 0389: dt=0.576000, rms=0.464 (0.001%), neg=0, invalid=762 0390: dt=0.576000, rms=0.464 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0391: dt=5.066667, rms=0.464 (0.167%), neg=0, invalid=762 0392: dt=4.032000, rms=0.464 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0393: dt=4.032000, rms=0.464 (0.017%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0394: dt=4.032000, rms=0.464 (-0.026%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 0395: dt=0.000060, rms=0.472 (0.101%), neg=0, invalid=762 0396: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 0397: dt=1.280000, rms=0.471 (0.204%), neg=0, invalid=762 0398: dt=0.448000, rms=0.471 (0.016%), neg=0, invalid=762 0399: dt=0.448000, rms=0.471 (0.009%), neg=0, invalid=762 0400: dt=0.448000, rms=0.471 (-0.015%), 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=0.463, neg=0, invalid=762 iter 0, gcam->neg = 697 after 15 iterations, nbhd size=1, neg = 0 0401: dt=1.870968, rms=0.440 (4.885%), neg=0, invalid=762 0402: dt=0.007000, rms=0.440 (0.008%), neg=0, invalid=762 0403: dt=0.007000, rms=0.440 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=762 0404: dt=0.096000, rms=0.440 (0.195%), neg=0, invalid=762 0405: dt=0.000438, rms=0.440 (0.007%), neg=0, invalid=762 0406: dt=0.000438, rms=0.440 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0407: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0408: dt=92.480000, rms=0.429 (0.014%), neg=0, invalid=762 0409: dt=129.472000, rms=0.429 (0.007%), neg=0, invalid=762 0410: dt=129.472000, rms=0.429 (0.002%), neg=0, invalid=762 0411: dt=129.472000, rms=0.429 (0.004%), neg=0, invalid=762 0412: dt=129.472000, rms=0.429 (0.002%), neg=0, invalid=762 0413: dt=129.472000, rms=0.429 (0.002%), neg=0, invalid=762 0414: dt=129.472000, rms=0.429 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0415: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=762 0416: dt=145.152000, rms=0.429 (0.089%), neg=0, invalid=762 0417: dt=103.680000, rms=0.428 (0.042%), neg=0, invalid=762 0418: dt=103.680000, rms=0.428 (0.005%), neg=0, invalid=762 0419: dt=103.680000, rms=0.428 (0.074%), neg=0, invalid=762 0420: dt=103.680000, rms=0.428 (0.040%), neg=0, invalid=762 0421: dt=103.680000, rms=0.428 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0422: dt=6.400000, rms=0.428 (0.033%), neg=0, invalid=762 0423: dt=0.700000, rms=0.428 (0.001%), neg=0, invalid=762 0424: dt=0.700000, rms=0.428 (0.000%), neg=0, invalid=762 0425: dt=0.700000, rms=0.428 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0426: dt=93.288136, rms=0.425 (0.680%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0427: dt=22.235294, rms=0.424 (0.235%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0428: dt=22.235294, rms=0.424 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0429: dt=22.235294, rms=0.424 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0430: dt=22.235294, rms=0.423 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0431: dt=22.235294, rms=0.422 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0432: dt=22.235294, rms=0.421 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0433: dt=22.235294, rms=0.421 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 12 iterations, nbhd size=1, neg = 0 0434: dt=22.235294, rms=0.420 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 0435: dt=22.235294, rms=0.420 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0436: dt=38.400000, rms=0.420 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=0, neg = 0 0437: dt=38.400000, rms=0.420 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 5 iterations, nbhd size=0, neg = 0 0438: dt=38.400000, rms=0.419 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 46 after 7 iterations, nbhd size=0, neg = 0 0439: dt=38.400000, rms=0.419 (0.028%), neg=0, invalid=762 iter 0, gcam->neg = 39 after 6 iterations, nbhd size=0, neg = 0 0440: dt=38.400000, rms=0.419 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 15 iterations, nbhd size=1, neg = 0 0441: dt=38.400000, rms=0.419 (0.036%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0442: dt=0.000422, rms=0.422 (0.000%), neg=0, invalid=762 0443: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 iter 0, gcam->neg = 4 after 12 iterations, nbhd size=1, neg = 0 0444: dt=7.506173, rms=0.422 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0445: dt=14.352941, rms=0.422 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 77 after 18 iterations, nbhd size=1, neg = 0 0446: dt=34.813187, rms=0.421 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 95 after 15 iterations, nbhd size=1, neg = 0 0447: dt=29.052632, rms=0.420 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 210 after 25 iterations, nbhd size=1, neg = 0 0448: dt=29.052632, rms=0.420 (-0.568%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0449: dt=0.000050, rms=0.426 (0.000%), neg=0, invalid=762 0450: dt=0.000000, rms=0.426 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0451: dt=0.000000, rms=0.426 (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=0.417, neg=0, invalid=762 iter 0, gcam->neg = 508 after 14 iterations, nbhd size=1, neg = 0 0452: dt=1.068138, rms=0.409 (1.766%), neg=0, invalid=762 0453: dt=0.000027, rms=0.409 (0.000%), neg=0, invalid=762 0454: dt=0.000027, 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 0455: dt=0.192000, rms=0.409 (0.142%), neg=0, invalid=762 0456: dt=0.320000, rms=0.408 (0.126%), neg=0, invalid=762 0457: dt=0.320000, rms=0.408 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 59 after 9 iterations, nbhd size=1, neg = 0 0458: dt=0.320000, rms=0.407 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 52 after 16 iterations, nbhd size=1, neg = 0 0459: dt=0.320000, rms=0.407 (0.036%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0460: dt=0.320000, rms=0.407 (0.061%), neg=0, invalid=762 0461: dt=0.320000, rms=0.407 (0.048%), neg=0, invalid=762 0462: dt=0.320000, rms=0.407 (0.026%), neg=0, invalid=762 0463: dt=0.320000, rms=0.406 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0464: dt=0.320000, rms=0.406 (0.048%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0465: dt=0.320000, rms=0.406 (0.025%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 42 minutes and 28 seconds. mri_ca_register utimesec 14246.964132 mri_ca_register stimesec 10.876346 mri_ca_register ru_maxrss 1340380 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5262993 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 65112 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4241 mri_ca_register ru_nivcsw 19184 FSRUNTIME@ mri_ca_register 3.7078 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 22:25:47 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-573 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-6.0.0/0050006/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 7.11 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 = 0.09072 (22) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (485 voxels, overlap=0.766) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (485 voxels, peak = 22), gca=21.9 gca peak = 0.17677 (13) mri peak = 0.09707 (22) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (549 voxels, overlap=0.414) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (549 voxels, peak = 19), gca=19.0 gca peak = 0.28129 (95) mri peak = 0.10693 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (823 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (823 voxels, peak = 92), gca=91.7 gca peak = 0.16930 (96) mri peak = 0.13614 (93) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (858 voxels, overlap=0.971) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (858 voxels, peak = 94), gca=93.6 gca peak = 0.24553 (55) mri peak = 0.10943 (67) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1057 voxels, overlap=0.278) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1057 voxels, peak = 64), gca=63.5 gca peak = 0.30264 (59) mri peak = 0.08655 (64) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (969 voxels, overlap=0.561) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (969 voxels, peak = 65), gca=64.6 gca peak = 0.07580 (103) mri peak = 0.13466 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, overlap=0.595) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, peak = 103), gca=103.0 gca peak = 0.07714 (104) mri peak = 0.13371 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, peak = 104), gca=104.0 gca peak = 0.09712 (58) mri peak = 0.05172 (66) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (47831 voxels, overlap=0.795) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (47831 voxels, peak = 66), gca=65.8 gca peak = 0.11620 (58) mri peak = 0.05170 (63) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (45145 voxels, overlap=0.739) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (45145 voxels, peak = 65), gca=64.7 gca peak = 0.30970 (66) mri peak = 0.14346 (76) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1080 voxels, overlap=0.166) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1080 voxels, peak = 74), gca=74.2 gca peak = 0.15280 (69) mri peak = 0.16741 (77) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1007 voxels, overlap=0.594) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1007 voxels, peak = 71), gca=70.7 gca peak = 0.13902 (56) mri peak = 0.05015 (61) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (38897 voxels, overlap=0.914) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (38897 voxels, peak = 62), gca=62.4 gca peak = 0.14777 (55) mri peak = 0.05034 (61) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35319 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35319 voxels, peak = 59), gca=58.6 gca peak = 0.16765 (84) mri peak = 0.06262 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5000 voxels, overlap=0.623) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5000 voxels, peak = 93), gca=92.8 gca peak = 0.18739 (84) mri peak = 0.06800 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5255 voxels, overlap=0.673) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5255 voxels, peak = 93), gca=92.8 gca peak = 0.29869 (57) mri peak = 0.09751 (67) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (523 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (523 voxels, peak = 66), gca=66.4 gca peak = 0.33601 (57) mri peak = 0.08288 (71) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (540 voxels, overlap=0.057) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (540 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.07651 (87) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5090 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5090 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.08171 (87) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (4738 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (4738 voxels, peak = 86), gca=85.9 gca peak = 0.08324 (81) mri peak = 0.09787 (82) Left_Putamen (12): linear fit = 1.03 x + 0.0 (2062 voxels, overlap=0.705) Left_Putamen (12): linear fit = 1.03 x + 0.0 (2062 voxels, peak = 84), gca=83.8 gca peak = 0.10360 (77) mri peak = 0.09535 (81) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, overlap=0.748) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, peak = 80), gca=79.7 gca peak = 0.08424 (78) mri peak = 0.07595 (93) Brain_Stem (16): linear fit = 1.13 x + 0.0 (10892 voxels, overlap=0.278) Brain_Stem (16): linear fit = 1.13 x + 0.0 (10892 voxels, peak = 89), gca=88.5 gca peak = 0.12631 (89) mri peak = 0.05955 (94) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1519 voxels, overlap=0.754) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1519 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.07319 (95) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1577 voxels, overlap=0.901) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1577 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.08855 (20) gca peak = 0.19357 (14) mri peak = 0.15054 (21) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (87 voxels, overlap=0.849) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (87 voxels, peak = 14), gca=14.5 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 CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.14 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.20 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16968 (22) mri peak = 0.09072 (22) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (485 voxels, overlap=0.799) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (485 voxels, peak = 23), gca=22.5 gca peak = 0.12269 (18) mri peak = 0.09707 (22) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (549 voxels, overlap=0.684) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (549 voxels, peak = 18), gca=18.0 gca peak = 0.24779 (91) mri peak = 0.10693 (92) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (823 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (823 voxels, peak = 91), gca=90.5 gca peak = 0.20154 (94) mri peak = 0.13614 (93) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (858 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (858 voxels, peak = 94), gca=93.5 gca peak = 0.24791 (64) mri peak = 0.10943 (67) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1057 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1057 voxels, peak = 63), gca=63.0 gca peak = 0.22572 (65) mri peak = 0.08655 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (969 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (969 voxels, peak = 65), gca=65.0 gca peak = 0.07581 (103) mri peak = 0.13466 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, overlap=0.595) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45644 voxels, peak = 103), gca=103.0 gca peak = 0.07714 (104) mri peak = 0.13371 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46888 voxels, peak = 104), gca=104.0 gca peak = 0.08621 (66) mri peak = 0.05172 (66) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (47831 voxels, overlap=0.977) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (47831 voxels, peak = 65), gca=65.0 gca peak = 0.10555 (65) mri peak = 0.05170 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45145 voxels, overlap=0.965) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45145 voxels, peak = 65), gca=65.0 gca peak = 0.25483 (75) mri peak = 0.14346 (76) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1080 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1080 voxels, peak = 75), gca=75.0 gca peak = 0.15167 (70) mri peak = 0.16741 (77) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1007 voxels, overlap=0.715) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1007 voxels, peak = 70), gca=70.0 gca peak = 0.12891 (62) mri peak = 0.05015 (61) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (38897 voxels, overlap=0.998) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (38897 voxels, peak = 61), gca=61.1 gca peak = 0.13819 (58) mri peak = 0.05034 (61) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (35319 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (35319 voxels, peak = 59), gca=59.4 gca peak = 0.14189 (93) mri peak = 0.06262 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5000 voxels, overlap=0.980) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5000 voxels, peak = 93), gca=92.5 gca peak = 0.16472 (93) mri peak = 0.06800 (91) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5255 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5255 voxels, peak = 92), gca=91.6 gca peak = 0.30333 (68) mri peak = 0.09751 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (523 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (523 voxels, peak = 68), gca=68.0 gca peak = 0.29912 (68) mri peak = 0.08288 (71) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (540 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (540 voxels, peak = 67), gca=67.0 gca peak = 0.11133 (86) mri peak = 0.07651 (87) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5090 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5090 voxels, peak = 86), gca=85.6 gca peak = 0.10043 (86) mri peak = 0.08171 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4738 voxels, overlap=0.973) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4738 voxels, peak = 86), gca=86.0 gca peak = 0.08229 (84) mri peak = 0.09787 (82) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2062 voxels, overlap=0.835) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2062 voxels, peak = 85), gca=85.3 gca peak = 0.10883 (78) mri peak = 0.09535 (81) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2306 voxels, overlap=0.857) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2306 voxels, peak = 79), gca=79.2 gca peak = 0.07777 (89) mri peak = 0.07595 (93) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10892 voxels, overlap=0.816) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10892 voxels, peak = 89), gca=89.4 gca peak = 0.11370 (96) mri peak = 0.05955 (94) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1519 voxels, overlap=0.881) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1519 voxels, peak = 96), gca=95.5 gca peak = 0.16198 (91) mri peak = 0.07319 (95) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1577 voxels, overlap=0.965) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1577 voxels, peak = 90), gca=89.6 gca peak = 0.16785 (31) mri peak = 0.08855 (20) gca peak = 0.18343 (17) mri peak = 0.15054 (21) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (87 voxels, overlap=0.859) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (87 voxels, peak = 20), gca=19.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16329 (35) gca peak Left_Thalamus = 0.64095 (101) gca peak Third_Ventricle = 0.16785 (31) gca peak CSF = 0.19138 (43) gca peak Left_Accumbens_area = 0.88917 (64) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.18678 (27) gca peak Right_Accumbens_area = 0.30005 (73) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14524 (37) gca peak Fifth_Ventricle = 0.65271 (38) gca peak WM_hypointensities = 0.07965 (76) gca peak non_WM_hypointensities = 0.08569 (76) gca peak Optic_Chiasm = 0.70851 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.06 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 64856 voxels changed in iteration 0 of unlikely voxel relabeling 432 voxels changed in iteration 1 of unlikely voxel relabeling 21 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 51500 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels) 530 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 68534 changed. image ll: -2.111, PF=0.500 pass 2: 17938 changed. image ll: -2.110, PF=0.500 pass 3: 5861 changed. pass 4: 2219 changed. 43092 voxels changed in iteration 0 of unlikely voxel relabeling 330 voxels changed in iteration 1 of unlikely voxel relabeling 53 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8778 voxels changed in iteration 0 of unlikely voxel relabeling 171 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6596 voxels changed in iteration 0 of unlikely voxel relabeling 83 voxels changed in iteration 1 of unlikely voxel relabeling 45 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5887 voxels changed in iteration 0 of unlikely voxel relabeling 16 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 3682.938108 mri_ca_label stimesec 1.682744 mri_ca_label ru_maxrss 2094028 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 698207 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 65104 mri_ca_label ru_oublock 464 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 270 mri_ca_label ru_nivcsw 4759 auto-labeling took 60 minutes and 37 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/transforms/cc_up.lta 0050006 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-6.0.0/0050006/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/norm.mgz 78469 voxels in left wm, 70753 in right wm, xrange [119, 133] searching rotation angles z=[-1 13], y=[-5 9] 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 searching scale 1 Z rot 9.8 searching scale 1 Z rot 10.1 searching scale 1 Z rot 10.3 searching scale 1 Z rot 10.6 searching scale 1 Z rot 10.8 searching scale 1 Z rot 11.1 searching scale 1 Z rot 11.3 searching scale 1 Z rot 11.6 searching scale 1 Z rot 11.8 searching scale 1 Z rot 12.1 searching scale 1 Z rot 12.3 searching scale 1 Z rot 12.6 searching scale 1 Z rot 12.8 global minimum found at slice 125.0, rotations (1.81, 6.09) final transformation (x=125.0, yr=1.805, zr=6.087): 0.99387 -0.10604 0.03133 11.16102; 0.10599 0.99436 0.00334 10.95006; -0.03150 -0.00000 0.99950 15.99569; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 104 116 eigenvectors: 0.00099 -0.00060 1.00000; -0.07342 -0.99730 -0.00053; 0.99730 -0.07342 -0.00103; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aseg.auto.mgz... corpus callosum segmentation took 1.5 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 23:27:57 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 23:27:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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... 978 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 71 (71), valley at 23 (23) csf peak at 36, setting threshold to 59 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 71 (71), valley at 23 (23) csf peak at 36, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 53 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 23:30:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1682152 voxels in mask (pct= 10.03) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 23:30:52 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 (102.0): 102.3 +- 7.0 [79.0 --> 125.0] GM (73.0) : 71.5 +- 8.9 [30.0 --> 95.0] setting bottom of white matter range to 80.4 setting top of gray matter range to 89.3 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... 6846 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3552 filled 3106 bright non-wm voxels segmented. 2576 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.44 minutes reading wm segmentation from wm.seg.mgz... 76 voxels added to wm to prevent paths from MTL structures to cortex 2541 additional wm voxels added 0 additional wm voxels added SEG EDIT: 31668 voxels turned on, 32540 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 20 found - 20 modified | TOTAL: 20 pass 2 (xy+): 0 found - 20 modified | TOTAL: 20 pass 1 (xy-): 23 found - 23 modified | TOTAL: 43 pass 2 (xy-): 0 found - 23 modified | TOTAL: 43 pass 1 (yz+): 30 found - 30 modified | TOTAL: 73 pass 2 (yz+): 0 found - 30 modified | TOTAL: 73 pass 1 (yz-): 27 found - 27 modified | TOTAL: 100 pass 2 (yz-): 0 found - 27 modified | TOTAL: 100 pass 1 (xz+): 12 found - 12 modified | TOTAL: 112 pass 2 (xz+): 0 found - 12 modified | TOTAL: 112 pass 1 (xz-): 23 found - 23 modified | TOTAL: 135 pass 2 (xz-): 0 found - 23 modified | TOTAL: 135 Iteration Number : 1 pass 1 (+++): 44 found - 44 modified | TOTAL: 44 pass 2 (+++): 0 found - 44 modified | TOTAL: 44 pass 1 (+++): 28 found - 28 modified | TOTAL: 72 pass 2 (+++): 0 found - 28 modified | TOTAL: 72 pass 1 (+++): 52 found - 52 modified | TOTAL: 124 pass 2 (+++): 0 found - 52 modified | TOTAL: 124 pass 1 (+++): 42 found - 42 modified | TOTAL: 166 pass 2 (+++): 0 found - 42 modified | TOTAL: 166 Iteration Number : 1 pass 1 (++): 104 found - 104 modified | TOTAL: 104 pass 2 (++): 0 found - 104 modified | TOTAL: 104 pass 1 (+-): 128 found - 128 modified | TOTAL: 232 pass 2 (+-): 0 found - 128 modified | TOTAL: 232 pass 1 (--): 105 found - 105 modified | TOTAL: 337 pass 2 (--): 0 found - 105 modified | TOTAL: 337 pass 1 (-+): 132 found - 132 modified | TOTAL: 469 pass 2 (-+): 0 found - 132 modified | TOTAL: 469 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 5 found - 5 modified | TOTAL: 14 pass 2 (xy-): 0 found - 5 modified | TOTAL: 14 pass 1 (yz+): 13 found - 13 modified | TOTAL: 27 pass 2 (yz+): 0 found - 13 modified | TOTAL: 27 pass 1 (yz-): 3 found - 3 modified | TOTAL: 30 pass 2 (yz-): 0 found - 3 modified | TOTAL: 30 pass 1 (xz+): 3 found - 3 modified | TOTAL: 33 pass 2 (xz+): 0 found - 3 modified | TOTAL: 33 pass 1 (xz-): 8 found - 8 modified | TOTAL: 41 pass 2 (xz-): 0 found - 8 modified | TOTAL: 41 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 4 found - 4 modified | TOTAL: 7 pass 2 (+-): 0 found - 4 modified | TOTAL: 7 pass 1 (--): 2 found - 2 modified | TOTAL: 9 pass 2 (--): 0 found - 2 modified | TOTAL: 9 pass 1 (-+): 5 found - 5 modified | TOTAL: 14 pass 2 (-+): 0 found - 5 modified | TOTAL: 14 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 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 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 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 : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 850 (out of 580398: 0.146451) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 23:33:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 1.02888 -0.08054 0.02819 2.08265; 0.07035 1.11927 0.19553 -47.67914; -0.05470 -0.18472 0.93780 31.91875; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.02888 -0.08054 0.02819 2.08265; 0.07035 1.11927 0.19553 -47.67914; -0.05470 -0.18472 0.93780 31.91875; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2456 (min = 350, max = 1400), aspect = 1.34 (min = 0.10, max = 0.75) need search nearby using seed (125, 121, 151), TAL = (3.0, 23.0, 7.0) talairach voxel to voxel transform 0.96542 0.06253 -0.04206 2.31326; -0.06817 0.85930 -0.17711 46.76616; 0.04289 0.17290 1.02898 -24.68933; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 121, 151) --> (3.0, 23.0, 7.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (3.00, 23.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 23.00, 7.00) SRC: (106.83, 116.70, 156.20) search lh wm seed point around talairach space (-15.00, 23.00, 7.00), SRC: (141.58, 114.25, 157.74) 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 23:33:38 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 5 found - 5 modified | TOTAL: 12 pass 2 (xy-): 0 found - 5 modified | TOTAL: 12 pass 1 (yz+): 1 found - 1 modified | TOTAL: 13 pass 2 (yz+): 0 found - 1 modified | TOTAL: 13 pass 1 (yz-): 3 found - 3 modified | TOTAL: 16 pass 2 (yz-): 0 found - 3 modified | TOTAL: 16 pass 1 (xz+): 2 found - 2 modified | TOTAL: 18 pass 2 (xz+): 0 found - 2 modified | TOTAL: 18 pass 1 (xz-): 5 found - 5 modified | TOTAL: 23 pass 2 (xz-): 0 found - 5 modified | TOTAL: 23 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 3 found - 3 modified | TOTAL: 3 pass 2 (--): 0 found - 3 modified | TOTAL: 3 pass 1 (-+): 4 found - 4 modified | TOTAL: 7 pass 2 (-+): 0 found - 4 modified | TOTAL: 7 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 = 30 (out of 280687: 0.010688) 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 40: 2246 vertices, 2382 faces slice 50: 9265 vertices, 9530 faces slice 60: 17955 vertices, 18307 faces slice 70: 29001 vertices, 29361 faces slice 80: 39947 vertices, 40313 faces slice 90: 52117 vertices, 52572 faces slice 100: 65369 vertices, 65861 faces slice 110: 78563 vertices, 79032 faces slice 120: 91171 vertices, 91628 faces slice 130: 103292 vertices, 103769 faces slice 140: 115868 vertices, 116375 faces slice 150: 126398 vertices, 126837 faces slice 160: 135392 vertices, 135799 faces slice 170: 143602 vertices, 143962 faces slice 180: 150392 vertices, 150729 faces slice 190: 156453 vertices, 156732 faces slice 200: 160011 vertices, 160203 faces slice 210: 160614 vertices, 160722 faces slice 220: 160614 vertices, 160722 faces slice 230: 160614 vertices, 160722 faces slice 240: 160614 vertices, 160722 faces slice 250: 160614 vertices, 160722 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... 160614 voxel in cpt #1: X=-108 [v=160614,e=482166,f=321444] located at (-25.583124, -15.946038, 14.179648) For the whole surface: X=-108 [v=160614,e=482166,f=321444] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 23:33:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 4 found - 4 modified | TOTAL: 9 pass 2 (yz-): 0 found - 4 modified | TOTAL: 9 pass 1 (xz+): 1 found - 1 modified | TOTAL: 10 pass 2 (xz+): 0 found - 1 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 3 found - 3 modified | TOTAL: 3 pass 2 (--): 0 found - 3 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 277893: 0.005398) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 2642 vertices, 2824 faces slice 50: 10235 vertices, 10544 faces slice 60: 20000 vertices, 20380 faces slice 70: 31129 vertices, 31551 faces slice 80: 42855 vertices, 43229 faces slice 90: 54815 vertices, 55243 faces slice 100: 67830 vertices, 68286 faces slice 110: 80377 vertices, 80814 faces slice 120: 92596 vertices, 93064 faces slice 130: 104464 vertices, 104884 faces slice 140: 115812 vertices, 116329 faces slice 150: 126283 vertices, 126717 faces slice 160: 135533 vertices, 135910 faces slice 170: 143299 vertices, 143608 faces slice 180: 150104 vertices, 150398 faces slice 190: 155440 vertices, 155685 faces slice 200: 158605 vertices, 158745 faces slice 210: 158914 vertices, 159006 faces slice 220: 158914 vertices, 159006 faces slice 230: 158914 vertices, 159006 faces slice 240: 158914 vertices, 159006 faces slice 250: 158914 vertices, 159006 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... 158914 voxel in cpt #1: X=-92 [v=158914,e=477018,f=318012] located at (29.024014, -17.883068, 10.140586) For the whole surface: X=-92 [v=158914,e=477018,f=318012] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 23:33:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 23:33:49 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 27981 of (27981 27984) to complete... Waiting for PID 27984 of (27981 27984) 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 (27981 27984) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 23:33:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 23:33:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 28029 of (28029 28032) to complete... Waiting for PID 28032 of (28029 28032) 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 = 48.1 mm, total surface area = 83182 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.163 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.072 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.059 (target=0.015) step 040: RMS=0.056 (target=0.015) step 045: RMS=0.055 (target=0.015) step 050: RMS=0.053 (target=0.015) step 055: RMS=0.054 (target=0.015) step 060: RMS=0.054 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 47.735743 mris_inflate stimesec 0.106983 mris_inflate ru_maxrss 234328 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 33480 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11304 mris_inflate ru_oublock 11320 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2368 mris_inflate ru_nivcsw 3485 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.3 mm, total surface area = 82355 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 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=0.077 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.052 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.049 (target=0.015) step 050: RMS=0.048 (target=0.015) step 055: RMS=0.047 (target=0.015) step 060: RMS=0.047 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 47.129835 mris_inflate stimesec 0.103984 mris_inflate ru_maxrss 232148 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 33445 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11184 mris_inflate ru_oublock 11200 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2306 mris_inflate ru_nivcsw 3500 PIDs (28029 28032) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 23:34:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 23:34:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 28095 of (28095 28099) to complete... Waiting for PID 28099 of (28095 28099) 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 0.91 +- 0.56 (0.00-->7.11) (max @ vno 66493 --> 67872) face area 0.02 +- 0.03 (-0.21-->0.77) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.283... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.523, avgs=0 005/300: dt: 0.9000, rms radial error=177.262, avgs=0 010/300: dt: 0.9000, rms radial error=176.703, avgs=0 015/300: dt: 0.9000, rms radial error=175.969, avgs=0 020/300: dt: 0.9000, rms radial error=175.137, avgs=0 025/300: dt: 0.9000, rms radial error=174.243, avgs=0 030/300: dt: 0.9000, rms radial error=173.316, avgs=0 035/300: dt: 0.9000, rms radial error=172.372, avgs=0 040/300: dt: 0.9000, rms radial error=171.419, avgs=0 045/300: dt: 0.9000, rms radial error=170.464, avgs=0 050/300: dt: 0.9000, rms radial error=169.509, avgs=0 055/300: dt: 0.9000, rms radial error=168.557, avgs=0 060/300: dt: 0.9000, rms radial error=167.607, avgs=0 065/300: dt: 0.9000, rms radial error=166.662, avgs=0 070/300: dt: 0.9000, rms radial error=165.722, avgs=0 075/300: dt: 0.9000, rms radial error=164.787, avgs=0 080/300: dt: 0.9000, rms radial error=163.857, avgs=0 085/300: dt: 0.9000, rms radial error=162.933, avgs=0 090/300: dt: 0.9000, rms radial error=162.014, avgs=0 095/300: dt: 0.9000, rms radial error=161.101, avgs=0 100/300: dt: 0.9000, rms radial error=160.193, avgs=0 105/300: dt: 0.9000, rms radial error=159.289, avgs=0 110/300: dt: 0.9000, rms radial error=158.391, avgs=0 115/300: dt: 0.9000, rms radial error=157.497, avgs=0 120/300: dt: 0.9000, rms radial error=156.609, avgs=0 125/300: dt: 0.9000, rms radial error=155.725, avgs=0 130/300: dt: 0.9000, rms radial error=154.846, avgs=0 135/300: dt: 0.9000, rms radial error=153.971, avgs=0 140/300: dt: 0.9000, rms radial error=153.101, avgs=0 145/300: dt: 0.9000, rms radial error=152.236, avgs=0 150/300: dt: 0.9000, rms radial error=151.376, avgs=0 155/300: dt: 0.9000, rms radial error=150.521, avgs=0 160/300: dt: 0.9000, rms radial error=149.670, avgs=0 165/300: dt: 0.9000, rms radial error=148.825, avgs=0 170/300: dt: 0.9000, rms radial error=147.984, avgs=0 175/300: dt: 0.9000, rms radial error=147.147, avgs=0 180/300: dt: 0.9000, rms radial error=146.315, avgs=0 185/300: dt: 0.9000, rms radial error=145.488, avgs=0 190/300: dt: 0.9000, rms radial error=144.665, avgs=0 195/300: dt: 0.9000, rms radial error=143.847, avgs=0 200/300: dt: 0.9000, rms radial error=143.034, avgs=0 205/300: dt: 0.9000, rms radial error=142.225, avgs=0 210/300: dt: 0.9000, rms radial error=141.420, avgs=0 215/300: dt: 0.9000, rms radial error=140.621, avgs=0 220/300: dt: 0.9000, rms radial error=139.825, avgs=0 225/300: dt: 0.9000, rms radial error=139.034, avgs=0 230/300: dt: 0.9000, rms radial error=138.247, avgs=0 235/300: dt: 0.9000, rms radial error=137.465, avgs=0 240/300: dt: 0.9000, rms radial error=136.689, avgs=0 245/300: dt: 0.9000, rms radial error=135.917, avgs=0 250/300: dt: 0.9000, rms radial error=135.149, avgs=0 255/300: dt: 0.9000, rms radial error=134.386, avgs=0 260/300: dt: 0.9000, rms radial error=133.627, avgs=0 265/300: dt: 0.9000, rms radial error=132.872, avgs=0 270/300: dt: 0.9000, rms radial error=132.122, avgs=0 275/300: dt: 0.9000, rms radial error=131.376, avgs=0 280/300: dt: 0.9000, rms radial error=130.634, avgs=0 285/300: dt: 0.9000, rms radial error=129.896, avgs=0 290/300: dt: 0.9000, rms radial error=129.162, avgs=0 295/300: dt: 0.9000, rms radial error=128.433, avgs=0 300/300: dt: 0.9000, rms radial error=127.708, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19409.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3495.05 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 = 426.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00432 epoch 4 (K=640.0), pass 1, starting sse = 40.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00780 final distance error %29.56 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 283.006976 mris_sphere stimesec 0.225965 mris_sphere ru_maxrss 234540 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33542 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11344 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8538 mris_sphere ru_nivcsw 19180 FSRUNTIME@ mris_sphere 0.0771 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 0.92 +- 0.57 (0.00-->9.55) (max @ vno 95896 --> 97007) face area 0.02 +- 0.03 (-0.42-->0.50) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.285... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.349, avgs=0 005/300: dt: 0.9000, rms radial error=177.090, avgs=0 010/300: dt: 0.9000, rms radial error=176.533, avgs=0 015/300: dt: 0.9000, rms radial error=175.802, avgs=0 020/300: dt: 0.9000, rms radial error=174.970, avgs=0 025/300: dt: 0.9000, rms radial error=174.080, avgs=0 030/300: dt: 0.9000, rms radial error=173.156, avgs=0 035/300: dt: 0.9000, rms radial error=172.215, avgs=0 040/300: dt: 0.9000, rms radial error=171.267, avgs=0 045/300: dt: 0.9000, rms radial error=170.316, avgs=0 050/300: dt: 0.9000, rms radial error=169.367, avgs=0 055/300: dt: 0.9000, rms radial error=168.421, avgs=0 060/300: dt: 0.9000, rms radial error=167.478, avgs=0 065/300: dt: 0.9000, rms radial error=166.539, avgs=0 070/300: dt: 0.9000, rms radial error=165.605, avgs=0 075/300: dt: 0.9000, rms radial error=164.675, avgs=0 080/300: dt: 0.9000, rms radial error=163.751, avgs=0 085/300: dt: 0.9000, rms radial error=162.831, avgs=0 090/300: dt: 0.9000, rms radial error=161.916, avgs=0 095/300: dt: 0.9000, rms radial error=161.006, avgs=0 100/300: dt: 0.9000, rms radial error=160.101, avgs=0 105/300: dt: 0.9000, rms radial error=159.200, avgs=0 110/300: dt: 0.9000, rms radial error=158.305, avgs=0 115/300: dt: 0.9000, rms radial error=157.414, avgs=0 120/300: dt: 0.9000, rms radial error=156.529, avgs=0 125/300: dt: 0.9000, rms radial error=155.648, avgs=0 130/300: dt: 0.9000, rms radial error=154.772, avgs=0 135/300: dt: 0.9000, rms radial error=153.900, avgs=0 140/300: dt: 0.9000, rms radial error=153.034, avgs=0 145/300: dt: 0.9000, rms radial error=152.172, avgs=0 150/300: dt: 0.9000, rms radial error=151.314, avgs=0 155/300: dt: 0.9000, rms radial error=150.461, avgs=0 160/300: dt: 0.9000, rms radial error=149.613, avgs=0 165/300: dt: 0.9000, rms radial error=148.770, avgs=0 170/300: dt: 0.9000, rms radial error=147.934, avgs=0 175/300: dt: 0.9000, rms radial error=147.098, avgs=0 180/300: dt: 0.9000, rms radial error=146.268, avgs=0 185/300: dt: 0.9000, rms radial error=145.444, avgs=0 190/300: dt: 0.9000, rms radial error=144.623, avgs=0 195/300: dt: 0.9000, rms radial error=143.807, avgs=0 200/300: dt: 0.9000, rms radial error=142.996, avgs=0 205/300: dt: 0.9000, rms radial error=142.189, avgs=0 210/300: dt: 0.9000, rms radial error=141.386, avgs=0 215/300: dt: 0.9000, rms radial error=140.589, avgs=0 220/300: dt: 0.9000, rms radial error=139.797, avgs=0 225/300: dt: 0.9000, rms radial error=139.008, avgs=0 230/300: dt: 0.9000, rms radial error=138.224, avgs=0 235/300: dt: 0.9000, rms radial error=137.444, avgs=0 240/300: dt: 0.9000, rms radial error=136.669, avgs=0 245/300: dt: 0.9000, rms radial error=135.898, avgs=0 250/300: dt: 0.9000, rms radial error=135.132, avgs=0 255/300: dt: 0.9000, rms radial error=134.370, avgs=0 260/300: dt: 0.9000, rms radial error=133.610, avgs=0 265/300: dt: 0.9000, rms radial error=132.856, avgs=0 270/300: dt: 0.9000, rms radial error=132.106, avgs=0 275/300: dt: 0.9000, rms radial error=131.361, avgs=0 280/300: dt: 0.9000, rms radial error=130.620, avgs=0 285/300: dt: 0.9000, rms radial error=129.882, avgs=0 290/300: dt: 0.9000, rms radial error=129.150, avgs=0 295/300: dt: 0.9000, rms radial error=128.420, avgs=0 300/300: dt: 0.9000, rms radial error=127.696, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19143.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3424.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 414.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00325 epoch 4 (K=640.0), pass 1, starting sse = 38.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00622 final distance error %30.79 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 268.332207 mris_sphere stimesec 0.252961 mris_sphere ru_maxrss 232368 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33504 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11184 mris_sphere ru_oublock 11224 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8364 mris_sphere ru_nivcsw 19398 FSRUNTIME@ mris_sphere 0.0746 hours 1 threads PIDs (28095 28099) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 23:39:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 23:39:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 23:39:22 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 lh #@# Fix Topology rh Sat Oct 7 23:39:22 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 rh Waiting for PID 28615 of (28615 28618) to complete... Waiting for PID 28618 of (28615 28618) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 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=-108 (nv=160614, nf=321444, ne=482166, g=55) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 15866 ambiguous faces found in tessellation segmenting defects... 56 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 21 into 14 -merging segment 25 into 14 -merging segment 36 into 38 53 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1987 (-4.5994) -vertex loglikelihood: -5.8552 (-2.9276) -normal dot loglikelihood: -3.5753 (-3.5753) -quad curv loglikelihood: -6.2378 (-3.1189) Total Loglikelihood : -24.8670 CORRECTING DEFECT 0 (vertices=60, convex hull=95, v0=3826) After retessellation of defect 0 (v0=3826), euler #=-52 (151554,452337,300731) : difference with theory (-50) = 2 CORRECTING DEFECT 1 (vertices=21, convex hull=50, v0=4325) After retessellation of defect 1 (v0=4325), euler #=-51 (151562,452383,300770) : difference with theory (-49) = 2 CORRECTING DEFECT 2 (vertices=270, convex hull=235, v0=10444) After retessellation of defect 2 (v0=10444), euler #=-50 (151695,452892,301147) : difference with theory (-48) = 2 CORRECTING DEFECT 3 (vertices=27, convex hull=62, v0=12555) After retessellation of defect 3 (v0=12555), euler #=-49 (151704,452942,301189) : difference with theory (-47) = 2 CORRECTING DEFECT 4 (vertices=21, convex hull=24, v0=13306) After retessellation of defect 4 (v0=13306), euler #=-48 (151708,452958,301202) : difference with theory (-46) = 2 CORRECTING DEFECT 5 (vertices=78, convex hull=91, v0=14968) After retessellation of defect 5 (v0=14968), euler #=-47 (151722,453044,301275) : difference with theory (-45) = 2 CORRECTING DEFECT 6 (vertices=22, convex hull=66, v0=21129) After retessellation of defect 6 (v0=21129), euler #=-46 (151731,453095,301318) : difference with theory (-44) = 2 CORRECTING DEFECT 7 (vertices=21, convex hull=59, v0=40671) After retessellation of defect 7 (v0=40671), euler #=-45 (151741,453143,301357) : difference with theory (-43) = 2 CORRECTING DEFECT 8 (vertices=107, convex hull=37, v0=41801) After retessellation of defect 8 (v0=41801), euler #=-44 (151744,453167,301379) : difference with theory (-42) = 2 CORRECTING DEFECT 9 (vertices=56, convex hull=44, v0=49317) After retessellation of defect 9 (v0=49317), euler #=-43 (151748,453195,301404) : difference with theory (-41) = 2 CORRECTING DEFECT 10 (vertices=766, convex hull=289, v0=49763) After retessellation of defect 10 (v0=49763), euler #=-42 (151838,453607,301727) : difference with theory (-40) = 2 CORRECTING DEFECT 11 (vertices=39, convex hull=69, v0=54593) After retessellation of defect 11 (v0=54593), euler #=-41 (151865,453718,301812) : difference with theory (-39) = 2 CORRECTING DEFECT 12 (vertices=381, convex hull=222, v0=58001) After retessellation of defect 12 (v0=58001), euler #=-40 (151928,454020,302052) : difference with theory (-38) = 2 CORRECTING DEFECT 13 (vertices=15, convex hull=27, v0=63491) After retessellation of defect 13 (v0=63491), euler #=-39 (151935,454049,302075) : difference with theory (-37) = 2 CORRECTING DEFECT 14 (vertices=1511, convex hull=717, v0=63848) XL defect detected... After retessellation of defect 14 (v0=63848), euler #=-36 (152399,455822,303387) : difference with theory (-36) = 0 CORRECTING DEFECT 15 (vertices=22, convex hull=22, v0=74911) After retessellation of defect 15 (v0=74911), euler #=-35 (152402,455838,303401) : difference with theory (-35) = 0 CORRECTING DEFECT 16 (vertices=552, convex hull=155, v0=76707) After retessellation of defect 16 (v0=76707), euler #=-34 (152474,456124,303616) : difference with theory (-34) = 0 CORRECTING DEFECT 17 (vertices=10, convex hull=27, v0=79537) After retessellation of defect 17 (v0=79537), euler #=-33 (152476,456138,303629) : difference with theory (-33) = 0 CORRECTING DEFECT 18 (vertices=23, convex hull=47, v0=81151) After retessellation of defect 18 (v0=81151), euler #=-32 (152480,456173,303661) : difference with theory (-32) = 0 CORRECTING DEFECT 19 (vertices=10, convex hull=27, v0=81886) After retessellation of defect 19 (v0=81886), euler #=-31 (152485,456194,303678) : difference with theory (-31) = 0 CORRECTING DEFECT 20 (vertices=48, convex hull=27, v0=85509) After retessellation of defect 20 (v0=85509), euler #=-30 (152492,456227,303705) : difference with theory (-30) = 0 CORRECTING DEFECT 21 (vertices=42, convex hull=57, v0=88734) After retessellation of defect 21 (v0=88734), euler #=-29 (152495,456259,303735) : difference with theory (-29) = 0 CORRECTING DEFECT 22 (vertices=34, convex hull=21, v0=91490) After retessellation of defect 22 (v0=91490), euler #=-28 (152500,456282,303754) : difference with theory (-28) = 0 CORRECTING DEFECT 23 (vertices=829, convex hull=258, v0=94781) After retessellation of defect 23 (v0=94781), euler #=-27 (152588,456672,304057) : difference with theory (-27) = 0 CORRECTING DEFECT 24 (vertices=24, convex hull=41, v0=97771) After retessellation of defect 24 (v0=97771), euler #=-26 (152603,456736,304107) : difference with theory (-26) = 0 CORRECTING DEFECT 25 (vertices=950, convex hull=234, v0=97775) After retessellation of defect 25 (v0=97775), euler #=-25 (152638,456946,304283) : difference with theory (-25) = 0 CORRECTING DEFECT 26 (vertices=154, convex hull=79, v0=99562) After retessellation of defect 26 (v0=99562), euler #=-24 (152648,457010,304338) : difference with theory (-24) = 0 CORRECTING DEFECT 27 (vertices=21, convex hull=28, v0=100075) After retessellation of defect 27 (v0=100075), euler #=-23 (152652,457032,304357) : difference with theory (-23) = 0 CORRECTING DEFECT 28 (vertices=9, convex hull=29, v0=100543) After retessellation of defect 28 (v0=100543), euler #=-22 (152654,457047,304371) : difference with theory (-22) = 0 CORRECTING DEFECT 29 (vertices=27, convex hull=31, v0=101637) After retessellation of defect 29 (v0=101637), euler #=-21 (152656,457065,304388) : difference with theory (-21) = 0 CORRECTING DEFECT 30 (vertices=10, convex hull=26, v0=105322) After retessellation of defect 30 (v0=105322), euler #=-20 (152658,457080,304402) : difference with theory (-20) = 0 CORRECTING DEFECT 31 (vertices=32, convex hull=36, v0=105416) After retessellation of defect 31 (v0=105416), euler #=-19 (152668,457121,304434) : difference with theory (-19) = 0 CORRECTING DEFECT 32 (vertices=14, convex hull=29, v0=107803) After retessellation of defect 32 (v0=107803), euler #=-18 (152671,457138,304449) : difference with theory (-18) = 0 CORRECTING DEFECT 33 (vertices=135, convex hull=167, v0=109047) After retessellation of defect 33 (v0=109047), euler #=-18 (152744,457442,304680) : difference with theory (-17) = 1 CORRECTING DEFECT 34 (vertices=129, convex hull=106, v0=111588) After retessellation of defect 34 (v0=111588), euler #=-17 (152783,457609,304809) : difference with theory (-16) = 1 CORRECTING DEFECT 35 (vertices=1908, convex hull=685, v0=112772) XL defect detected... After retessellation of defect 35 (v0=112772), euler #=-15 (152851,458210,305344) : difference with theory (-15) = 0 CORRECTING DEFECT 36 (vertices=23, convex hull=32, v0=115400) After retessellation of defect 36 (v0=115400), euler #=-14 (152855,458232,305363) : difference with theory (-14) = 0 CORRECTING DEFECT 37 (vertices=106, convex hull=52, v0=129063) After retessellation of defect 37 (v0=129063), euler #=-13 (152871,458303,305419) : difference with theory (-13) = 0 CORRECTING DEFECT 38 (vertices=5, convex hull=15, v0=130165) After retessellation of defect 38 (v0=130165), euler #=-12 (152872,458309,305425) : difference with theory (-12) = 0 CORRECTING DEFECT 39 (vertices=49, convex hull=71, v0=132039) After retessellation of defect 39 (v0=132039), euler #=-11 (152899,458418,305508) : difference with theory (-11) = 0 CORRECTING DEFECT 40 (vertices=21, convex hull=30, v0=133544) After retessellation of defect 40 (v0=133544), euler #=-10 (152902,458436,305524) : difference with theory (-10) = 0 CORRECTING DEFECT 41 (vertices=28, convex hull=60, v0=133632) After retessellation of defect 41 (v0=133632), euler #=-9 (152911,458487,305567) : difference with theory (-9) = 0 CORRECTING DEFECT 42 (vertices=46, convex hull=82, v0=136164) After retessellation of defect 42 (v0=136164), euler #=-8 (152924,458561,305629) : difference with theory (-8) = 0 CORRECTING DEFECT 43 (vertices=38, convex hull=64, v0=137730) After retessellation of defect 43 (v0=137730), euler #=-7 (152942,458641,305692) : difference with theory (-7) = 0 CORRECTING DEFECT 44 (vertices=122, convex hull=56, v0=139984) After retessellation of defect 44 (v0=139984), euler #=-6 (152951,458697,305740) : difference with theory (-6) = 0 CORRECTING DEFECT 45 (vertices=60, convex hull=25, v0=143095) After retessellation of defect 45 (v0=143095), euler #=-5 (152957,458724,305762) : difference with theory (-5) = 0 CORRECTING DEFECT 46 (vertices=20, convex hull=51, v0=146351) After retessellation of defect 46 (v0=146351), euler #=-4 (152965,458767,305798) : difference with theory (-4) = 0 CORRECTING DEFECT 47 (vertices=50, convex hull=74, v0=150371) After retessellation of defect 47 (v0=150371), euler #=-3 (152977,458835,305855) : difference with theory (-3) = 0 CORRECTING DEFECT 48 (vertices=34, convex hull=87, v0=151922) After retessellation of defect 48 (v0=151922), euler #=-2 (152999,458936,305935) : difference with theory (-2) = 0 CORRECTING DEFECT 49 (vertices=52, convex hull=74, v0=154557) After retessellation of defect 49 (v0=154557), euler #=-1 (153019,459024,306004) : difference with theory (-1) = 0 CORRECTING DEFECT 50 (vertices=11, convex hull=26, v0=156893) After retessellation of defect 50 (v0=156893), euler #=0 (153021,459039,306018) : difference with theory (0) = 0 CORRECTING DEFECT 51 (vertices=13, convex hull=26, v0=160355) After retessellation of defect 51 (v0=160355), euler #=1 (153024,459056,306033) : difference with theory (1) = 0 CORRECTING DEFECT 52 (vertices=11, convex hull=28, v0=160590) After retessellation of defect 52 (v0=160590), euler #=2 (153025,459069,306046) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.03-->11.36) (max @ vno 121583 --> 126997) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.03-->11.36) (max @ vno 121583 --> 126997) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 198 mutations (32.9%), 404 crossovers (67.1%), 966 vertices were eliminated building final representation... 7589 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=153025, nf=306046, ne=459069, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 70.5 minutes 0 defective edges removing intersecting faces 000: 651 intersecting 001: 18 intersecting 002: 5 intersecting mris_fix_topology utimesec 4230.759826 mris_fix_topology stimesec 0.305953 mris_fix_topology ru_maxrss 530052 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 63828 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 22608 mris_fix_topology ru_oublock 14832 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 667 mris_fix_topology ru_nivcsw 9041 FSRUNTIME@ mris_fix_topology lh 1.1747 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050006 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=-92 (nv=158914, nf=318012, ne=477018, g=47) 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 12 iterations marking ambiguous vertices... 13495 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 7 into 4 30 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1832 (-4.5916) -vertex loglikelihood: -5.8634 (-2.9317) -normal dot loglikelihood: -3.6471 (-3.6471) -quad curv loglikelihood: -6.1569 (-3.0785) Total Loglikelihood : -24.8507 CORRECTING DEFECT 0 (vertices=71, convex hull=92, v0=158) After retessellation of defect 0 (v0=158), euler #=-25 (151242,451658,300391) : difference with theory (-27) = -2 CORRECTING DEFECT 1 (vertices=26, convex hull=53, v0=19594) After retessellation of defect 1 (v0=19594), euler #=-24 (151253,451713,300436) : difference with theory (-26) = -2 CORRECTING DEFECT 2 (vertices=9, convex hull=21, v0=27143) After retessellation of defect 2 (v0=27143), euler #=-23 (151253,451720,300444) : difference with theory (-25) = -2 CORRECTING DEFECT 3 (vertices=1954, convex hull=617, v0=36596) XL defect detected... After retessellation of defect 3 (v0=36596), euler #=-22 (151449,452625,301154) : difference with theory (-24) = -2 CORRECTING DEFECT 4 (vertices=1329, convex hull=670, v0=45991) XL defect detected... After retessellation of defect 4 (v0=45991), euler #=-20 (151789,454029,302220) : difference with theory (-23) = -3 CORRECTING DEFECT 5 (vertices=50, convex hull=66, v0=56055) After retessellation of defect 5 (v0=56055), euler #=-19 (151818,454145,302308) : difference with theory (-22) = -3 CORRECTING DEFECT 6 (vertices=389, convex hull=327, v0=82549) normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 3 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 3 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 3 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 3 faces normal vector of length zero at vertex 154914 with 3 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces normal vector of length zero at vertex 154914 with 4 faces After retessellation of defect 6 (v0=82549), euler #=-18 (151965,454752,302769) : difference with theory (-21) = -3 CORRECTING DEFECT 7 (vertices=188, convex hull=153, v0=86552) After retessellation of defect 7 (v0=86552), euler #=-17 (152008,454951,302926) : difference with theory (-20) = -3 CORRECTING DEFECT 8 (vertices=96, convex hull=125, v0=88132) After retessellation of defect 8 (v0=88132), euler #=-16 (152021,455049,303012) : difference with theory (-19) = -3 CORRECTING DEFECT 9 (vertices=27, convex hull=15, v0=99763) After retessellation of defect 9 (v0=99763), euler #=-15 (152022,455057,303020) : difference with theory (-18) = -3 CORRECTING DEFECT 10 (vertices=1102, convex hull=465, v0=108461) L defect detected... After retessellation of defect 10 (v0=108461), euler #=-16 (152279,456096,303801) : difference with theory (-17) = -1 CORRECTING DEFECT 11 (vertices=44, convex hull=91, v0=108594) After retessellation of defect 11 (v0=108594), euler #=-15 (152299,456199,303885) : difference with theory (-16) = -1 CORRECTING DEFECT 12 (vertices=911, convex hull=254, v0=109473) After retessellation of defect 12 (v0=109473), euler #=-14 (152382,456567,304171) : difference with theory (-15) = -1 CORRECTING DEFECT 13 (vertices=191, convex hull=93, v0=112780) After retessellation of defect 13 (v0=112780), euler #=-14 (152427,456743,304302) : difference with theory (-14) = 0 CORRECTING DEFECT 14 (vertices=314, convex hull=145, v0=115593) After retessellation of defect 14 (v0=115593), euler #=-13 (152460,456907,304434) : difference with theory (-13) = 0 CORRECTING DEFECT 15 (vertices=31, convex hull=59, v0=116463) After retessellation of defect 15 (v0=116463), euler #=-12 (152474,456974,304488) : difference with theory (-12) = 0 CORRECTING DEFECT 16 (vertices=55, convex hull=88, v0=118352) After retessellation of defect 16 (v0=118352), euler #=-11 (152504,457100,304585) : difference with theory (-11) = 0 CORRECTING DEFECT 17 (vertices=58, convex hull=43, v0=125173) After retessellation of defect 17 (v0=125173), euler #=-10 (152513,457145,304622) : difference with theory (-10) = 0 CORRECTING DEFECT 18 (vertices=168, convex hull=70, v0=126569) After retessellation of defect 18 (v0=126569), euler #=-9 (152526,457215,304680) : difference with theory (-9) = 0 CORRECTING DEFECT 19 (vertices=49, convex hull=42, v0=129221) After retessellation of defect 19 (v0=129221), euler #=-8 (152537,457264,304719) : difference with theory (-8) = 0 CORRECTING DEFECT 20 (vertices=112, convex hull=35, v0=131139) After retessellation of defect 20 (v0=131139), euler #=-7 (152538,457285,304740) : difference with theory (-7) = 0 CORRECTING DEFECT 21 (vertices=26, convex hull=58, v0=136509) After retessellation of defect 21 (v0=136509), euler #=-6 (152547,457334,304781) : difference with theory (-6) = 0 CORRECTING DEFECT 22 (vertices=65, convex hull=78, v0=141888) After retessellation of defect 22 (v0=141888), euler #=-5 (152563,457415,304847) : difference with theory (-5) = 0 CORRECTING DEFECT 23 (vertices=30, convex hull=27, v0=141911) After retessellation of defect 23 (v0=141911), euler #=-4 (152565,457428,304859) : difference with theory (-4) = 0 CORRECTING DEFECT 24 (vertices=114, convex hull=103, v0=145450) After retessellation of defect 24 (v0=145450), euler #=-3 (152586,457540,304951) : difference with theory (-3) = 0 CORRECTING DEFECT 25 (vertices=37, convex hull=94, v0=146732) After retessellation of defect 25 (v0=146732), euler #=-2 (152607,457641,305032) : difference with theory (-2) = 0 CORRECTING DEFECT 26 (vertices=49, convex hull=86, v0=150850) After retessellation of defect 26 (v0=150850), euler #=-1 (152635,457761,305125) : difference with theory (-1) = 0 CORRECTING DEFECT 27 (vertices=112, convex hull=141, v0=153022) After retessellation of defect 27 (v0=153022), euler #=0 (152681,457967,305286) : difference with theory (0) = 0 CORRECTING DEFECT 28 (vertices=50, convex hull=88, v0=155124) After retessellation of defect 28 (v0=155124), euler #=1 (152706,458079,305374) : difference with theory (1) = 0 CORRECTING DEFECT 29 (vertices=38, convex hull=84, v0=157208) After retessellation of defect 29 (v0=157208), euler #=2 (152724,458166,305444) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.02-->11.72) (max @ vno 83717 --> 93593) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.02-->11.72) (max @ vno 83717 --> 93593) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 82 mutations (31.1%), 182 crossovers (68.9%), 740 vertices were eliminated building final representation... 6190 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=152724, nf=305444, ne=458166, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 44.0 minutes 0 defective edges removing intersecting faces 000: 568 intersecting 001: 12 intersecting mris_fix_topology utimesec 2640.701552 mris_fix_topology stimesec 0.981850 mris_fix_topology ru_maxrss 512368 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 59154 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 22368 mris_fix_topology ru_oublock 14712 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 407 mris_fix_topology ru_nivcsw 4466 FSRUNTIME@ mris_fix_topology rh 0.7335 hours 1 threads PIDs (28615 28618) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 153025 - 459069 + 306046 = 2 --> 0 holes F =2V-4: 306046 = 306050-4 (0) 2E=3F: 918138 = 918138 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 152724 - 458166 + 305444 = 2 --> 0 holes F =2V-4: 305444 = 305448-4 (0) 2E=3F: 916332 = 916332 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 123 intersecting 001: 18 intersecting 002: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 132 intersecting 001: 9 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 00:50:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 00:50:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 rh Waiting for PID 1320 of (1320 1323) to complete... Waiting for PID 1323 of (1320 1323) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... 19474 bright wm thresholded. 3500 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.orig... computing class statistics... border white: 288670 voxels (1.72%) border gray 347901 voxels (2.07%) WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 52.8 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->7.04) (max @ vno 77459 --> 152075) face area 0.28 +- 0.14 (0.00-->8.73) mean absolute distance = 0.64 +- 0.80 5404 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+-5.2, GM=71+-6.1 mean inside = 94.2, mean outside = 78.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=83.3, 167 (167) missing vertices, mean dist 0.2 [0.5 (%42.0)->0.7 (%58.0))] %83 local maxima, %13 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 0.91 +- 0.25 (0.04-->7.15) (max @ vno 77459 --> 152075) face area 0.28 +- 0.14 (0.00-->10.04) mean absolute distance = 0.31 +- 0.51 3489 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2737872.2, rms=8.446 001: dt: 0.5000, sse=1601978.5, rms=5.807 (31.251%) 002: dt: 0.5000, sse=1160721.5, rms=4.345 (25.169%) 003: dt: 0.5000, sse=993428.0, rms=3.639 (16.258%) 004: dt: 0.5000, sse=917421.2, rms=3.263 (10.333%) 005: dt: 0.5000, sse=891752.8, rms=3.127 (4.161%) 006: dt: 0.5000, sse=871919.6, rms=3.012 (3.690%) rms = 2.98, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=868484.8, rms=2.985 (0.896%) 008: dt: 0.2500, sse=741577.9, rms=2.012 (32.589%) 009: dt: 0.2500, sse=720294.9, rms=1.836 (8.727%) rms = 1.80, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=715609.6, rms=1.797 (2.148%) rms = 1.77, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=713068.8, rms=1.773 (1.334%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.9, 137 (60) missing vertices, mean dist -0.2 [0.3 (%75.4)->0.3 (%24.6))] %89 local maxima, % 7 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 +- 0.24 (0.07-->7.16) (max @ vno 77459 --> 152075) face area 0.35 +- 0.17 (0.00-->13.66) mean absolute distance = 0.23 +- 0.38 3591 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1257121.0, rms=4.087 012: dt: 0.5000, sse=962587.1, rms=2.559 (37.377%) 013: dt: 0.5000, sse=941239.1, rms=2.448 (4.351%) rms = 2.43, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=937403.0, rms=2.429 (0.766%) 015: dt: 0.2500, sse=858673.9, rms=1.706 (29.761%) 016: dt: 0.2500, sse=839972.4, rms=1.557 (8.771%) rms = 1.52, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=837607.2, rms=1.520 (2.364%) rms = 1.49, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=832455.5, rms=1.492 (1.840%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 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 mean border=87.5, 157 (48) missing vertices, mean dist -0.1 [0.2 (%67.8)->0.2 (%32.2))] %91 local maxima, % 4 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 0.89 +- 0.25 (0.07-->7.15) (max @ vno 77459 --> 152075) face area 0.34 +- 0.17 (0.00-->13.94) mean absolute distance = 0.21 +- 0.32 3258 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=931380.2, rms=2.522 019: dt: 0.5000, sse=883103.1, rms=2.029 (19.566%) rms = 2.13, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=822568.7, rms=1.589 (21.685%) 021: dt: 0.2500, sse=820281.9, rms=1.383 (12.934%) 022: dt: 0.2500, sse=803458.6, rms=1.325 (4.240%) rms = 1.32, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=802911.9, rms=1.321 (0.291%) rms = 1.30, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=801105.9, rms=1.297 (1.781%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 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 removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.0, 159 (33) missing vertices, mean dist -0.0 [0.2 (%54.9)->0.2 (%45.1))] %93 local maxima, % 3 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-6.0.0/0050006/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=807180.8, rms=1.483 025: dt: 0.5000, sse=799083.2, rms=1.369 (7.704%) rms = 1.70, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=776283.5, rms=1.158 (15.442%) rms = 1.13, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=778308.6, rms=1.135 (2.006%) rms = 1.10, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=770976.8, rms=1.105 (2.639%) positioning took 0.6 minutes generating cortex label... 20 non-cortical segments detected only using segment with 7416 vertices erasing segment 0 (vno[0] = 37102) erasing segment 2 (vno[0] = 74662) erasing segment 3 (vno[0] = 90456) erasing segment 4 (vno[0] = 106432) erasing segment 5 (vno[0] = 106538) erasing segment 6 (vno[0] = 107647) erasing segment 7 (vno[0] = 107694) erasing segment 8 (vno[0] = 107698) erasing segment 9 (vno[0] = 108911) erasing segment 10 (vno[0] = 109987) erasing segment 11 (vno[0] = 110897) erasing segment 12 (vno[0] = 111828) erasing segment 13 (vno[0] = 112774) erasing segment 14 (vno[0] = 114550) erasing segment 15 (vno[0] = 123498) erasing segment 16 (vno[0] = 126692) erasing segment 17 (vno[0] = 128472) erasing segment 18 (vno[0] = 129161) erasing segment 19 (vno[0] = 129217) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.area vertex spacing 0.89 +- 0.25 (0.03-->7.07) (max @ vno 77459 --> 152075) face area 0.33 +- 0.17 (0.00-->13.83) refinement took 5.9 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... 19474 bright wm thresholded. 3500 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.orig... computing class statistics... border white: 288670 voxels (1.72%) border gray 347901 voxels (2.07%) WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 53.8 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->6.45) (max @ vno 106323 --> 152152) face area 0.28 +- 0.13 (0.00-->6.14) mean absolute distance = 0.62 +- 0.76 5103 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+-6.1, GM=72+-5.2 mean inside = 94.0, mean outside = 78.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.4, 102 (102) missing vertices, mean dist 0.2 [0.5 (%43.2)->0.7 (%56.8))] %81 local maxima, %15 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 0.91 +- 0.25 (0.08-->6.68) (max @ vno 106323 --> 152152) face area 0.28 +- 0.13 (0.00-->5.46) mean absolute distance = 0.30 +- 0.48 3451 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2656823.5, rms=8.274 001: dt: 0.5000, sse=1536624.8, rms=5.592 (32.408%) 002: dt: 0.5000, sse=1104104.9, rms=4.113 (26.455%) 003: dt: 0.5000, sse=942800.1, rms=3.390 (17.578%) 004: dt: 0.5000, sse=870693.2, rms=3.008 (11.255%) 005: dt: 0.5000, sse=844174.9, rms=2.857 (5.046%) 006: dt: 0.5000, sse=830967.4, rms=2.764 (3.236%) rms = 2.76, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=829254.0, rms=2.760 (0.134%) 008: dt: 0.2500, sse=701601.4, rms=1.678 (39.195%) 009: dt: 0.2500, sse=686544.6, rms=1.455 (13.285%) rms = 1.41, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=678947.2, rms=1.410 (3.148%) rms = 1.37, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=675191.9, rms=1.371 (2.708%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 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 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.9, 104 (45) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %88 local maxima, % 9 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 +- 0.24 (0.07-->6.39) (max @ vno 106323 --> 152152) face area 0.34 +- 0.16 (0.00-->6.95) mean absolute distance = 0.23 +- 0.35 4531 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1188095.6, rms=3.792 012: dt: 0.5000, sse=918986.5, rms=2.270 (40.154%) 013: dt: 0.5000, sse=907736.0, rms=2.196 (3.224%) rms = 2.19, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=900842.8, rms=2.189 (0.325%) 015: dt: 0.2500, sse=820975.2, rms=1.354 (38.142%) 016: dt: 0.2500, sse=809150.6, rms=1.217 (10.154%) rms = 1.21, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=808378.4, rms=1.207 (0.803%) rms = 1.17, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=805461.3, rms=1.168 (3.236%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.5, 110 (36) missing vertices, mean dist -0.1 [0.2 (%68.0)->0.2 (%32.0))] %91 local maxima, % 5 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 0.89 +- 0.24 (0.09-->6.32) (max @ vno 106323 --> 152152) face area 0.33 +- 0.16 (0.00-->6.88) mean absolute distance = 0.21 +- 0.30 4062 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=912179.8, rms=2.386 019: dt: 0.5000, sse=852922.6, rms=1.887 (20.941%) rms = 1.98, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=805822.6, rms=1.404 (25.601%) 021: dt: 0.2500, sse=789320.5, rms=1.168 (16.774%) 022: dt: 0.2500, sse=782370.5, rms=1.105 (5.387%) rms = 1.12, time step reduction 2 of 3 to 0.125... rms = 1.09, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=780965.1, rms=1.089 (1.454%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 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 mean border=88.1, 115 (31) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %92 local maxima, % 3 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-6.0.0/0050006/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=788040.1, rms=1.312 024: dt: 0.5000, sse=785306.8, rms=1.257 (4.129%) rms = 1.65, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=764289.4, rms=0.962 (23.511%) rms = 0.92, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=766876.1, rms=0.918 (4.592%) 027: dt: 0.1250, sse=761314.9, rms=0.863 (5.944%) rms = 0.85, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=756585.7, rms=0.848 (1.781%) positioning took 0.7 minutes generating cortex label... 16 non-cortical segments detected only using segment with 6801 vertices erasing segment 0 (vno[0] = 42361) erasing segment 1 (vno[0] = 42398) erasing segment 2 (vno[0] = 46842) erasing segment 4 (vno[0] = 69635) erasing segment 5 (vno[0] = 93981) erasing segment 6 (vno[0] = 108364) erasing segment 7 (vno[0] = 109341) erasing segment 8 (vno[0] = 109469) erasing segment 9 (vno[0] = 109484) erasing segment 10 (vno[0] = 111496) erasing segment 11 (vno[0] = 111547) erasing segment 12 (vno[0] = 113607) erasing segment 13 (vno[0] = 115193) erasing segment 14 (vno[0] = 152183) erasing segment 15 (vno[0] = 152419) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->6.19) (max @ vno 106323 --> 152152) face area 0.33 +- 0.16 (0.00-->6.86) refinement took 6.1 minutes PIDs (1320 1323) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 00:56:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 00:56:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 1529 of (1529 1532) to complete... Waiting for PID 1532 of (1529 1532) 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 (1529 1532) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 00:56:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 00:56:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 1576 of (1576 1579) to complete... Waiting for PID 1579 of (1576 1579) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.7 mm, total surface area = 92052 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.039 (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=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 1.2 minutes mris_inflate utimesec 69.078498 mris_inflate stimesec 0.162975 mris_inflate ru_maxrss 223720 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32489 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11984 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2287 mris_inflate ru_nivcsw 7023 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.8 mm, total surface area = 91378 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.053 (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=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 1.3 minutes mris_inflate utimesec 86.152902 mris_inflate stimesec 0.286956 mris_inflate ru_maxrss 223560 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32451 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5328 mris_inflate ru_nivcsw 5282 PIDs (1576 1579) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 00:57:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun Oct 8 00:57:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 1782 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1785 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1788 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1791 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1794 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1797 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1800 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1803 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1806 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1809 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1813 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... Waiting for PID 1816 of (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 0.707*4pi (8.888) --> 0 handles ICI = 188.0, FI = 1974.2, variation=31086.455 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 204 vertices thresholded to be in k1 ~ [-0.20 0.45], k2 ~ [-0.09 0.06] total integrated curvature = 0.537*4pi (6.745) --> 0 handles ICI = 1.5, FI = 9.2, variation=159.135 120 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 140 vertices thresholded to be in [-0.11 0.16] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021 done. mris_curvature -w rh.white.preaparc total integrated curvature = 2.385*4pi (29.966) --> -1 handles ICI = 196.0, FI = 2254.9, variation=34871.325 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 203 vertices thresholded to be in k1 ~ [-0.26 0.35], k2 ~ [-0.10 0.06] total integrated curvature = 0.493*4pi (6.195) --> 1 handles ICI = 1.4, FI = 10.3, variation=169.243 134 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 156 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022 done. PIDs (1782 1785 1788 1791 1794 1797 1800 1803 1806 1809 1813 1816) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 00:59:19 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050006 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 [ 0050006/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 [ 325 ] Gb_filter = 0 WARN: S lookup min: -0.051931 WARN: S explicit min: 0.000000 vertex = 249 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 00:59:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050006 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 [ 0050006/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 [ 265 ] Gb_filter = 0 WARN: S lookup min: -0.067015 WARN: S explicit min: 0.000000 vertex = 96 #-------------------------------------------- #@# Sphere lh Sun Oct 8 00:59:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 00:59:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 2016 of (2016 2020) to complete... Waiting for PID 2020 of (2016 2020) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0.265... 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 %20.37 pass 1: epoch 2 of 3 starting distance error %20.23 unfolding complete - removing small folds... starting distance error %20.17 removing remaining folds... final distance error %20.19 MRISunfold() return, current seed 1234 -01: dt=0.0000, 154 negative triangles 159: dt=0.9900, 154 negative triangles 160: dt=0.9900, 84 negative triangles 161: dt=0.9900, 61 negative triangles 162: dt=0.9900, 55 negative triangles 163: dt=0.9900, 43 negative triangles 164: dt=0.9900, 40 negative triangles 165: dt=0.9900, 35 negative triangles 166: dt=0.9900, 37 negative triangles 167: dt=0.9900, 31 negative triangles 168: dt=0.9900, 29 negative triangles 169: dt=0.9900, 31 negative triangles 170: dt=0.9900, 24 negative triangles 171: dt=0.9900, 27 negative triangles 172: dt=0.9900, 20 negative triangles 173: dt=0.9900, 18 negative triangles 174: dt=0.9900, 20 negative triangles 175: dt=0.9900, 13 negative triangles 176: dt=0.9900, 12 negative triangles 177: dt=0.9900, 11 negative triangles 178: dt=0.9900, 12 negative triangles 179: dt=0.9900, 6 negative triangles 180: dt=0.9900, 8 negative triangles 181: dt=0.9900, 6 negative triangles 182: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.13 hours mris_sphere utimesec 4078.326000 mris_sphere stimesec 1.913709 mris_sphere ru_maxrss 311248 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 54496 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10808 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 134372 mris_sphere ru_nivcsw 336179 FSRUNTIME@ mris_sphere 1.1325 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0.267... 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 %20.87 pass 1: epoch 2 of 3 starting distance error %20.78 unfolding complete - removing small folds... starting distance error %20.70 removing remaining folds... final distance error %20.72 MRISunfold() return, current seed 1234 -01: dt=0.0000, 138 negative triangles 185: dt=0.9900, 138 negative triangles 186: dt=0.9900, 73 negative triangles 187: dt=0.9900, 56 negative triangles 188: dt=0.9900, 58 negative triangles 189: dt=0.9900, 58 negative triangles 190: dt=0.9900, 52 negative triangles 191: dt=0.9900, 57 negative triangles 192: dt=0.9900, 62 negative triangles 193: dt=0.9900, 60 negative triangles 194: dt=0.9900, 50 negative triangles 195: dt=0.9900, 52 negative triangles 196: dt=0.9900, 55 negative triangles 197: dt=0.9900, 50 negative triangles 198: dt=0.9900, 46 negative triangles 199: dt=0.9900, 46 negative triangles 200: dt=0.9900, 42 negative triangles 201: dt=0.9900, 32 negative triangles 202: dt=0.9900, 36 negative triangles 203: dt=0.9900, 32 negative triangles 204: dt=0.9900, 30 negative triangles 205: dt=0.9900, 33 negative triangles 206: dt=0.9900, 33 negative triangles 207: dt=0.9900, 29 negative triangles 208: dt=0.9900, 28 negative triangles 209: dt=0.9900, 33 negative triangles 210: dt=0.9900, 27 negative triangles 211: dt=0.9900, 24 negative triangles 212: dt=0.9900, 24 negative triangles 213: dt=0.9900, 23 negative triangles 214: dt=0.9900, 22 negative triangles 215: dt=0.9900, 26 negative triangles 216: dt=0.9900, 23 negative triangles 217: dt=0.9900, 19 negative triangles 218: dt=0.9900, 18 negative triangles 219: dt=0.9900, 18 negative triangles 220: dt=0.9900, 15 negative triangles 221: dt=0.9900, 15 negative triangles 222: dt=0.9900, 14 negative triangles 223: dt=0.9900, 17 negative triangles 224: dt=0.9900, 15 negative triangles 225: dt=0.9900, 15 negative triangles 226: dt=0.9900, 15 negative triangles 227: dt=0.9900, 12 negative triangles 228: dt=0.9900, 14 negative triangles 229: dt=0.9900, 13 negative triangles 230: dt=0.9900, 17 negative triangles 231: dt=0.9900, 17 negative triangles 232: dt=0.9900, 15 negative triangles 233: dt=0.9900, 13 negative triangles 234: dt=0.9900, 10 negative triangles 235: dt=0.9900, 11 negative triangles 236: dt=0.9900, 13 negative triangles 237: dt=0.9900, 11 negative triangles 238: dt=0.9900, 11 negative triangles 239: dt=0.9900, 11 negative triangles 240: dt=0.9900, 7 negative triangles 241: dt=0.9900, 11 negative triangles 242: dt=0.9900, 10 negative triangles 243: dt=0.9900, 8 negative triangles 244: dt=0.9900, 9 negative triangles 245: dt=0.9900, 8 negative triangles 246: dt=0.9900, 9 negative triangles 247: dt=0.9900, 8 negative triangles 248: dt=0.9900, 8 negative triangles 249: dt=0.9900, 3 negative triangles 250: dt=0.9900, 3 negative triangles 251: dt=0.9900, 2 negative triangles 252: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.17 hours mris_sphere utimesec 4320.467189 mris_sphere stimesec 1.813724 mris_sphere ru_maxrss 314308 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 55262 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10792 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 132392 mris_sphere ru_nivcsw 342765 FSRUNTIME@ mris_sphere 1.1689 hours 1 threads PIDs (2016 2020) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 02:09:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sun Oct 8 02:09:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 7879 of (7879 7882) to complete... Waiting for PID 7882 of (7879 7882) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 5.608 curvature mean = 0.007, std = 0.816 curvature mean = 0.022, std = 0.853 Starting MRISrigidBodyAlignGlobal() d=16.00 min @ (4.00, 0.00, 0.00) sse = 232989.9, tmin=3.5675 d=8.00 min @ (-2.00, 0.00, 2.00) sse = 232185.1, tmin=4.7817 d=4.00 min @ (1.00, 0.00, -1.00) sse = 227551.9, tmin=6.0289 d=2.00 min @ (0.00, 0.50, 0.00) sse = 227404.2, tmin=7.2737 d=1.00 min @ (0.25, 0.00, 0.00) sse = 227180.6, tmin=8.5104 d=0.50 min @ (-0.12, -0.12, 0.12) sse = 227132.3, tmin=9.7379 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 9.74 min curvature mean = -0.015, std = 0.825 curvature mean = 0.009, std = 0.940 curvature mean = -0.018, std = 0.834 curvature mean = 0.003, std = 0.975 curvature mean = -0.018, std = 0.836 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.030, std = 0.297 curvature mean = 0.035, std = 0.244 curvature mean = 0.074, std = 0.325 curvature mean = 0.033, std = 0.302 curvature mean = 0.039, std = 0.520 curvature mean = 0.033, std = 0.328 curvature mean = 0.021, std = 0.667 curvature mean = 0.033, std = 0.339 curvature mean = 0.008, std = 0.778 MRISregister() return, current seed 0 -01: dt=0.0000, 49 negative triangles 122: dt=0.9900, 49 negative triangles expanding nbhd size to 1 123: dt=0.9900, 72 negative triangles 124: dt=0.9900, 53 negative triangles 125: dt=0.9900, 62 negative triangles 126: dt=0.9900, 59 negative triangles 127: dt=0.9900, 55 negative triangles 128: dt=0.9900, 53 negative triangles 129: dt=0.9900, 49 negative triangles 130: dt=0.9900, 42 negative triangles 131: dt=0.9900, 37 negative triangles 132: dt=0.9900, 38 negative triangles 133: dt=0.9900, 33 negative triangles 134: dt=0.9900, 32 negative triangles 135: dt=0.9900, 27 negative triangles 136: dt=0.9900, 23 negative triangles 137: dt=0.9900, 24 negative triangles 138: dt=0.9900, 22 negative triangles 139: dt=0.9900, 15 negative triangles 140: dt=0.9900, 19 negative triangles 141: dt=0.9900, 13 negative triangles 142: dt=0.9900, 13 negative triangles 143: dt=0.9900, 10 negative triangles 144: dt=0.9900, 13 negative triangles 145: dt=0.9900, 9 negative triangles 146: dt=0.9900, 9 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 8 negative triangles 149: dt=0.9900, 7 negative triangles 150: dt=0.9900, 12 negative triangles 151: dt=0.9900, 10 negative triangles 152: dt=0.9900, 6 negative triangles 153: dt=0.9900, 7 negative triangles 154: dt=0.9900, 5 negative triangles 155: dt=0.9900, 7 negative triangles 156: dt=0.9900, 5 negative triangles 157: dt=0.9900, 7 negative triangles 158: dt=0.9900, 6 negative triangles 159: dt=0.9900, 6 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, 3 negative triangles 164: dt=0.9900, 3 negative triangles 165: dt=0.9900, 5 negative triangles 166: dt=0.9900, 3 negative triangles 167: dt=0.9900, 2 negative triangles 168: dt=0.9900, 4 negative triangles 169: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.73 hours mris_register utimesec 6228.721090 mris_register stimesec 5.315191 mris_register ru_maxrss 277876 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 39558 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10856 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 323678 mris_register ru_nivcsw 352562 FSRUNTIME@ mris_register 1.7308 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 5.627 curvature mean = 0.013, std = 0.801 curvature mean = 0.024, std = 0.853 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, 8.00) sse = 280927.8, tmin=2.3841 d=8.00 min @ (-2.00, -2.00, -2.00) sse = 268219.4, tmin=4.7867 d=4.00 min @ (1.00, 0.00, 0.00) sse = 267522.8, tmin=6.0133 d=2.00 min @ (0.00, 0.50, 0.00) sse = 267054.6, tmin=7.2351 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 266968.7, tmin=8.4627 d=0.50 min @ (0.00, 0.12, 0.12) sse = 266888.7, tmin=9.7011 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 9.70 min curvature mean = -0.022, std = 0.804 curvature mean = 0.008, std = 0.939 curvature mean = -0.027, std = 0.811 curvature mean = 0.003, std = 0.975 curvature mean = -0.029, std = 0.812 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.031, std = 0.311 curvature mean = 0.028, std = 0.236 curvature mean = 0.068, std = 0.319 curvature mean = 0.026, std = 0.294 curvature mean = 0.040, std = 0.501 curvature mean = 0.026, std = 0.321 curvature mean = 0.022, std = 0.640 curvature mean = 0.026, std = 0.332 curvature mean = 0.009, std = 0.746 MRISregister() return, current seed 0 -01: dt=0.0000, 57 negative triangles 120: dt=0.9900, 57 negative triangles expanding nbhd size to 1 121: dt=0.9900, 79 negative triangles 122: dt=0.9900, 54 negative triangles 123: dt=0.9900, 51 negative triangles 124: dt=0.9900, 57 negative triangles 125: dt=0.9900, 54 negative triangles 126: dt=0.9900, 49 negative triangles 127: dt=0.9900, 50 negative triangles 128: dt=0.9900, 52 negative triangles 129: dt=0.9900, 47 negative triangles 130: dt=0.9900, 45 negative triangles 131: dt=0.9900, 46 negative triangles 132: dt=0.9900, 38 negative triangles 133: dt=0.9900, 39 negative triangles 134: dt=0.9900, 34 negative triangles 135: dt=0.9900, 36 negative triangles 136: dt=0.9900, 29 negative triangles 137: dt=0.9900, 29 negative triangles 138: dt=0.9900, 27 negative triangles 139: dt=0.9900, 24 negative triangles 140: dt=0.9900, 29 negative triangles 141: dt=0.9900, 26 negative triangles 142: dt=0.9900, 23 negative triangles 143: dt=0.9900, 14 negative triangles 144: dt=0.9900, 11 negative triangles 145: dt=0.9900, 8 negative triangles 146: dt=0.9900, 8 negative triangles 147: dt=0.9900, 9 negative triangles 148: dt=0.9900, 5 negative triangles 149: dt=0.9900, 7 negative triangles 150: dt=0.9900, 4 negative triangles 151: dt=0.9900, 3 negative triangles 152: dt=0.9900, 4 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.91 hours mris_register utimesec 7252.648429 mris_register stimesec 6.846959 mris_register ru_maxrss 278452 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 40659 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10832 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 395255 mris_register ru_nivcsw 336185 FSRUNTIME@ mris_register 1.9088 hours 1 threads PIDs (7879 7882) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 04:04:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 04:04:08 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 14950 of (14950 14953) to complete... Waiting for PID 14953 of (14950 14953) 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 (14950 14953) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 04:04:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 04:04:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 14997 of (14997 15000) to complete... Waiting for PID 15000 of (14997 15000) 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 (14997 15000) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 04:04:13 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 04:04:13 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 15043 of (15043 15046) to complete... Waiting for PID 15046 of (15043 15046) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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... 1571 labels changed using aseg relabeling using gibbs priors... 000: 3405 changed, 153025 examined... 001: 845 changed, 14179 examined... 002: 197 changed, 4661 examined... 003: 74 changed, 1220 examined... 004: 26 changed, 448 examined... 005: 22 changed, 161 examined... 006: 4 changed, 133 examined... 007: 0 changed, 24 examined... 286 labels changed using aseg 000: 136 total segments, 93 labels (382 vertices) changed 001: 46 total segments, 3 labels (4 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2017 vertices marked for relabeling... 2017 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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... 1530 labels changed using aseg relabeling using gibbs priors... 000: 2989 changed, 152724 examined... 001: 703 changed, 12779 examined... 002: 159 changed, 3945 examined... 003: 54 changed, 963 examined... 004: 19 changed, 350 examined... 005: 5 changed, 116 examined... 006: 2 changed, 38 examined... 007: 0 changed, 10 examined... 156 labels changed using aseg 000: 104 total segments, 66 labels (326 vertices) changed 001: 41 total segments, 3 labels (6 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1734 vertices marked for relabeling... 1734 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 16 seconds. PIDs (15043 15046) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 04:04:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 04:04:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 rh Waiting for PID 15230 of (15230 15233) to complete... Waiting for PID 15233 of (15230 15233) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... 19474 bright wm thresholded. 3500 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.orig... computing class statistics... border white: 288670 voxels (1.72%) border gray 347901 voxels (2.07%) WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 52.8 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=71+-6.1 mean inside = 94.2, mean outside = 78.2 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 (0.03-->7.07) (max @ vno 77459 --> 152075) face area 0.33 +- 0.17 (0.00-->13.71) mean absolute distance = 0.55 +- 0.79 4669 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 108 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 146 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown deleting segment 8 with 22 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 47 points - only 0.00% unknown deleting segment 11 with 16 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown deleting segment 13 with 89 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown mean border=82.9, 194 (189) missing vertices, mean dist 0.4 [0.6 (%16.2)->0.5 (%83.8))] %82 local maxima, %14 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 (0.07-->7.08) (max @ vno 77459 --> 152075) face area 0.33 +- 0.17 (0.00-->12.59) mean absolute distance = 0.32 +- 0.52 3271 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2075721.1, rms=6.765 001: dt: 0.5000, sse=1200676.5, rms=4.006 (40.783%) 002: dt: 0.5000, sse=968008.8, rms=2.881 (28.091%) 003: dt: 0.5000, sse=926051.4, rms=2.613 (9.297%) 004: dt: 0.5000, sse=899295.0, rms=2.466 (5.616%) rms = 2.56, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=832619.7, rms=1.892 (23.271%) 006: dt: 0.2500, sse=806595.8, rms=1.608 (15.015%) 007: dt: 0.2500, sse=801238.6, rms=1.541 (4.169%) rms = 1.51, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=798399.7, rms=1.506 (2.293%) rms = 1.46, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=794388.6, rms=1.463 (2.821%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 127 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 55 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown deleting segment 8 with 23 points - only 0.00% unknown deleting segment 9 with 13 points - only 0.00% unknown deleting segment 10 with 17 points - only 0.00% unknown deleting segment 11 with 33 points - only 0.00% unknown deleting segment 12 with 12 points - only 0.00% unknown deleting segment 13 with 78 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown mean border=85.8, 167 (70) missing vertices, mean dist -0.2 [0.3 (%78.2)->0.2 (%21.8))] %89 local maxima, % 7 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 (0.09-->7.05) (max @ vno 77459 --> 152075) face area 0.35 +- 0.18 (0.00-->14.49) mean absolute distance = 0.23 +- 0.38 3627 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1254533.9, rms=4.017 010: dt: 0.5000, sse=940914.5, rms=2.298 (42.789%) 011: dt: 0.5000, sse=917445.9, rms=2.137 (7.015%) rms = 2.14, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=857901.1, rms=1.598 (25.216%) 013: dt: 0.2500, sse=835324.1, rms=1.280 (19.895%) rms = 1.23, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=834137.2, rms=1.231 (3.875%) rms = 1.19, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=824504.8, rms=1.195 (2.903%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 127 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 58 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 27 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 18 points - only 0.00% unknown deleting segment 10 with 39 points - only 0.00% unknown deleting segment 11 with 17 points - only 0.00% unknown deleting segment 12 with 72 points - only 20.83% unknown deleting segment 13 with 79 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown mean border=87.4, 167 (52) missing vertices, mean dist -0.1 [0.2 (%68.4)->0.2 (%31.6))] %92 local maxima, % 4 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 0.89 +- 0.25 (0.06-->7.08) (max @ vno 77459 --> 152075) face area 0.34 +- 0.18 (0.00-->14.44) mean absolute distance = 0.21 +- 0.33 3435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=919985.6, rms=2.386 016: dt: 0.5000, sse=861556.2, rms=1.875 (21.428%) rms = 1.99, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=813718.8, rms=1.393 (25.690%) 018: dt: 0.2500, sse=796317.3, rms=1.157 (16.941%) rms = 1.12, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=792110.2, rms=1.119 (3.288%) rms = 1.10, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=791668.9, rms=1.103 (1.411%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 130 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 69 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 47 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 18 points - only 0.00% unknown deleting segment 9 with 45 points - only 0.00% unknown deleting segment 10 with 19 points - only 0.00% unknown deleting segment 11 with 72 points - only 20.83% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 79 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown mean border=88.0, 184 (42) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))] %93 local maxima, % 3 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-6.0.0/0050006/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=799669.9, rms=1.353 021: dt: 0.5000, sse=794534.5, rms=1.223 (9.597%) rms = 1.57, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=777377.6, rms=0.984 (19.509%) rms = 0.94, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=774450.8, rms=0.944 (4.087%) rms = 0.93, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=772762.3, rms=0.934 (1.053%) positioning took 0.5 minutes generating cortex label... 23 non-cortical segments detected only using segment with 7397 vertices erasing segment 0 (vno[0] = 35908) erasing segment 2 (vno[0] = 65028) erasing segment 3 (vno[0] = 67491) erasing segment 4 (vno[0] = 74662) erasing segment 5 (vno[0] = 90456) erasing segment 6 (vno[0] = 102824) erasing segment 7 (vno[0] = 106432) erasing segment 8 (vno[0] = 106567) erasing segment 9 (vno[0] = 107694) erasing segment 10 (vno[0] = 107726) erasing segment 11 (vno[0] = 108911) erasing segment 12 (vno[0] = 109903) erasing segment 13 (vno[0] = 109987) erasing segment 14 (vno[0] = 111828) erasing segment 15 (vno[0] = 112678) erasing segment 16 (vno[0] = 112774) erasing segment 17 (vno[0] = 113616) erasing segment 18 (vno[0] = 114550) erasing segment 19 (vno[0] = 123498) erasing segment 20 (vno[0] = 129161) erasing segment 21 (vno[0] = 129216) erasing segment 22 (vno[0] = 129270) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.area vertex spacing 0.89 +- 0.26 (0.03-->6.98) (max @ vno 77459 --> 152075) face area 0.33 +- 0.18 (0.00-->14.12) 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 83 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=61.7, 163 (163) missing vertices, mean dist 1.2 [0.6 (%0.0)->3.6 (%100.0))] %12 local maxima, %21 large gradients and %63 min vals, 283 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=22235186.0, rms=27.089 001: dt: 0.0500, sse=19704072.0, rms=25.445 (6.068%) 002: dt: 0.0500, sse=17905706.0, rms=24.209 (4.857%) 003: dt: 0.0500, sse=16534452.0, rms=23.223 (4.075%) 004: dt: 0.0500, sse=15428163.0, rms=22.395 (3.564%) 005: dt: 0.0500, sse=14500116.0, rms=21.676 (3.210%) 006: dt: 0.0500, sse=13698389.0, rms=21.035 (2.956%) 007: dt: 0.0500, sse=12990610.0, rms=20.453 (2.769%) 008: dt: 0.0500, sse=12356911.0, rms=19.917 (2.621%) 009: dt: 0.0500, sse=11781887.0, rms=19.418 (2.507%) 010: dt: 0.0500, sse=11255720.0, rms=18.949 (2.412%) positioning took 1.1 minutes mean border=61.4, 132 (71) missing vertices, mean dist 1.1 [0.6 (%0.0)->3.1 (%100.0))] %13 local maxima, %21 large gradients and %62 min vals, 239 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=12173746.0, rms=19.758 011: dt: 0.0500, sse=11683745.0, rms=19.330 (2.166%) 012: dt: 0.0500, sse=11229690.0, rms=18.925 (2.097%) 013: dt: 0.0500, sse=10807222.0, rms=18.539 (2.035%) 014: dt: 0.0500, sse=10413641.0, rms=18.173 (1.975%) 015: dt: 0.0500, sse=10045978.0, rms=17.824 (1.920%) 016: dt: 0.0500, sse=9702392.0, rms=17.492 (1.865%) 017: dt: 0.0500, sse=9380718.0, rms=17.175 (1.814%) 018: dt: 0.0500, sse=9079002.0, rms=16.871 (1.764%) 019: dt: 0.0500, sse=8796039.0, rms=16.582 (1.715%) 020: dt: 0.0500, sse=8530628.0, rms=16.306 (1.665%) positioning took 1.1 minutes mean border=61.3, 175 (51) missing vertices, mean dist 1.0 [0.1 (%0.3)->2.8 (%99.7))] %13 local maxima, %22 large gradients and %61 min vals, 255 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=8649533.0, rms=16.437 021: dt: 0.0500, sse=8397825.0, rms=16.173 (1.607%) 022: dt: 0.0500, sse=8161398.0, rms=15.920 (1.560%) 023: dt: 0.0500, sse=7938880.5, rms=15.679 (1.515%) 024: dt: 0.0500, sse=7729375.0, rms=15.448 (1.471%) 025: dt: 0.0500, sse=7532066.0, rms=15.228 (1.427%) 026: dt: 0.0500, sse=7345766.0, rms=15.017 (1.387%) 027: dt: 0.0500, sse=7169365.0, rms=14.814 (1.351%) 028: dt: 0.0500, sse=7002075.5, rms=14.619 (1.317%) 029: dt: 0.0500, sse=6843180.0, rms=14.431 (1.285%) 030: dt: 0.0500, sse=6691885.5, rms=14.249 (1.256%) positioning took 1.1 minutes mean border=61.2, 215 (37) missing vertices, mean dist 0.9 [0.1 (%2.6)->2.6 (%97.4))] %13 local maxima, %22 large gradients and %61 min vals, 260 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=6782491.0, rms=14.360 031: dt: 0.5000, sse=5700381.0, rms=13.000 (9.474%) 032: dt: 0.5000, sse=4922298.5, rms=11.918 (8.317%) 033: dt: 0.5000, sse=4327131.5, rms=11.016 (7.567%) 034: dt: 0.5000, sse=3831588.2, rms=10.202 (7.395%) 035: dt: 0.5000, sse=3397759.0, rms=9.431 (7.553%) 036: dt: 0.5000, sse=2989004.0, rms=8.643 (8.357%) 037: dt: 0.5000, sse=2611181.0, rms=7.848 (9.196%) 038: dt: 0.5000, sse=2283338.8, rms=7.088 (9.692%) 039: dt: 0.5000, sse=2027349.8, rms=6.434 (9.230%) 040: dt: 0.5000, sse=1843114.9, rms=5.917 (8.031%) 041: dt: 0.5000, sse=1714173.6, rms=5.528 (6.573%) 042: dt: 0.5000, sse=1627641.5, rms=5.249 (5.052%) 043: dt: 0.5000, sse=1566138.0, rms=5.044 (3.907%) 044: dt: 0.5000, sse=1529266.4, rms=4.914 (2.577%) 045: dt: 0.5000, sse=1503782.6, rms=4.822 (1.860%) 046: dt: 0.5000, sse=1487359.1, rms=4.762 (1.255%) 047: dt: 0.5000, sse=1472893.0, rms=4.709 (1.098%) rms = 4.67, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1463779.5, rms=4.673 (0.768%) 049: dt: 0.2500, sse=1399507.8, rms=4.389 (6.083%) 050: dt: 0.2500, sse=1378363.2, rms=4.305 (1.910%) rms = 4.32, time step reduction 2 of 3 to 0.125... rms = 4.28, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1371940.2, rms=4.276 (0.667%) positioning took 3.4 minutes mean border=60.9, 5064 (20) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.7 (%54.4))] %19 local maxima, %18 large gradients and %55 min vals, 146 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=1577696.2, rms=4.297 052: dt: 0.5000, sse=1544609.1, rms=4.177 (2.797%) 053: dt: 0.5000, sse=1500392.4, rms=4.010 (3.992%) rms = 4.17, time step reduction 1 of 3 to 0.250... 054: dt: 0.2500, sse=1439485.6, rms=3.700 (7.721%) 055: dt: 0.2500, sse=1431768.9, rms=3.649 (1.394%) rms = 3.68, time step reduction 2 of 3 to 0.125... rms = 3.62, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1425851.0, rms=3.617 (0.884%) positioning took 1.2 minutes mean border=60.7, 5769 (15) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.5 (%55.4))] %24 local maxima, %14 large gradients and %54 min vals, 246 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=1441488.6, rms=3.704 rms = 4.04, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1423730.9, rms=3.614 (2.446%) rms = 3.64, time step reduction 2 of 3 to 0.125... rms = 3.60, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1421701.1, rms=3.602 (0.318%) positioning took 0.7 minutes mean border=60.4, 10871 (15) missing vertices, mean dist 0.1 [0.2 (%42.4)->0.4 (%57.6))] %26 local maxima, %11 large gradients and %51 min vals, 263 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-6.0.0/0050006/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1436238.1, rms=3.677 rms = 3.64, time step reduction 1 of 3 to 0.250... 059: dt: 0.5000, sse=1417560.0, rms=3.643 (0.923%) 060: dt: 0.2500, sse=1374928.1, rms=3.423 (6.041%) 061: dt: 0.2500, sse=1350653.0, rms=3.309 (3.335%) rms = 3.30, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1347627.8, rms=3.298 (0.329%) 063: dt: 0.1250, sse=1318916.4, rms=3.136 (4.915%) rms = 3.10, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1312231.6, rms=3.103 (1.046%) positioning took 1.4 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.area.pial vertex spacing 1.01 +- 0.46 (0.04-->8.60) (max @ vno 99895 --> 98711) face area 0.40 +- 0.33 (0.00-->8.78) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 153025 vertices processed 25000 of 153025 vertices processed 50000 of 153025 vertices processed 75000 of 153025 vertices processed 100000 of 153025 vertices processed 125000 of 153025 vertices processed 150000 of 153025 vertices processed 0 of 153025 vertices processed 25000 of 153025 vertices processed 50000 of 153025 vertices processed 75000 of 153025 vertices processed 100000 of 153025 vertices processed 125000 of 153025 vertices processed 150000 of 153025 vertices processed thickness calculation complete, 1100:2208 truncations. 28114 vertices at 0 distance 92828 vertices at 1 distance 93976 vertices at 2 distance 48520 vertices at 3 distance 19121 vertices at 4 distance 6669 vertices at 5 distance 2280 vertices at 6 distance 875 vertices at 7 distance 347 vertices at 8 distance 186 vertices at 9 distance 102 vertices at 10 distance 81 vertices at 11 distance 61 vertices at 12 distance 62 vertices at 13 distance 44 vertices at 14 distance 22 vertices at 15 distance 23 vertices at 16 distance 19 vertices at 17 distance 8 vertices at 18 distance 15 vertices at 19 distance 13 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.thickness positioning took 17.4 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050006 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-6.0.0/0050006/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... 19474 bright wm thresholded. 3500 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.orig... computing class statistics... border white: 288670 voxels (1.72%) border gray 347901 voxels (2.07%) WM (98.0): 98.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.3 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.9 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 53.8 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=72+-5.2 mean inside = 94.0, mean outside = 78.1 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 (0.03-->6.19) (max @ vno 106323 --> 152152) face area 0.33 +- 0.16 (0.00-->6.80) mean absolute distance = 0.54 +- 0.77 3722 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 40 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 7 points - only 0.00% unknown deleting segment 7 with 100 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 39 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown deleting segment 15 with 32 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown deleting segment 18 with 9 points - only 0.00% unknown mean border=83.0, 165 (165) missing vertices, mean dist 0.4 [0.6 (%15.8)->0.5 (%84.2))] %79 local maxima, %17 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 0.91 +- 0.25 (0.06-->5.94) (max @ vno 151609 --> 151552) face area 0.33 +- 0.16 (0.00-->6.30) mean absolute distance = 0.31 +- 0.49 3108 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2002834.9, rms=6.579 001: dt: 0.5000, sse=1168329.0, rms=3.866 (41.242%) 002: dt: 0.5000, sse=945729.2, rms=2.754 (28.760%) 003: dt: 0.5000, sse=912597.3, rms=2.543 (7.650%) 004: dt: 0.5000, sse=884369.5, rms=2.377 (6.541%) rms = 2.50, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=816359.1, rms=1.760 (25.935%) 006: dt: 0.2500, sse=792347.1, rms=1.475 (16.202%) 007: dt: 0.2500, sse=787284.1, rms=1.409 (4.453%) rms = 1.38, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=785247.1, rms=1.377 (2.338%) rms = 1.35, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=782843.9, rms=1.347 (2.110%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 41 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 4 points - only 0.00% unknown deleting segment 5 with 44 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 22 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown deleting segment 13 with 13 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 15 points - only 0.00% unknown mean border=85.8, 133 (56) missing vertices, mean dist -0.2 [0.3 (%76.9)->0.2 (%23.1))] %87 local maxima, % 9 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 (0.06-->6.13) (max @ vno 151609 --> 151552) face area 0.35 +- 0.17 (0.00-->7.08) mean absolute distance = 0.23 +- 0.35 4626 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1210182.0, rms=3.837 010: dt: 0.5000, sse=926547.0, rms=2.220 (42.148%) 011: dt: 0.5000, sse=908255.2, rms=2.108 (5.048%) rms = 2.12, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=847593.5, rms=1.533 (27.246%) 013: dt: 0.2500, sse=822406.8, rms=1.205 (21.433%) rms = 1.16, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=819837.1, rms=1.158 (3.900%) rms = 1.12, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=816615.6, rms=1.122 (3.098%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 25 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 44 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 38 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown deleting segment 13 with 15 points - only 0.00% unknown mean border=87.5, 106 (36) missing vertices, mean dist -0.1 [0.2 (%68.4)->0.2 (%31.6))] %91 local maxima, % 5 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 0.89 +- 0.25 (0.06-->6.16) (max @ vno 151609 --> 151552) face area 0.34 +- 0.17 (0.00-->6.91) mean absolute distance = 0.21 +- 0.30 4201 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=919439.4, rms=2.388 016: dt: 0.5000, sse=865029.1, rms=1.878 (21.327%) rms = 1.96, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=812689.7, rms=1.385 (26.265%) 018: dt: 0.2500, sse=793599.2, rms=1.146 (17.281%) 019: dt: 0.2500, sse=788036.3, rms=1.072 (6.402%) rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=786417.6, rms=1.056 (1.545%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 46 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 21 points - only 0.00% unknown deleting segment 8 with 58 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 44 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 15 points - only 0.00% unknown mean border=88.0, 113 (30) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))] %93 local maxima, % 4 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-6.0.0/0050006/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=793853.4, rms=1.305 rms = 1.26, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=803175.3, rms=1.256 (3.782%) 022: dt: 0.2500, sse=779353.4, rms=0.978 (22.154%) 023: dt: 0.2500, sse=766539.1, rms=0.896 (8.406%) rms = 0.92, time step reduction 2 of 3 to 0.125... rms = 0.86, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=764261.8, rms=0.862 (3.724%) positioning took 0.5 minutes generating cortex label... 15 non-cortical segments detected only using segment with 6826 vertices erasing segment 0 (vno[0] = 41284) erasing segment 1 (vno[0] = 45796) erasing segment 3 (vno[0] = 69635) erasing segment 4 (vno[0] = 93981) erasing segment 5 (vno[0] = 108364) erasing segment 6 (vno[0] = 109341) erasing segment 7 (vno[0] = 109469) erasing segment 8 (vno[0] = 109484) erasing segment 9 (vno[0] = 111496) erasing segment 10 (vno[0] = 111547) erasing segment 11 (vno[0] = 112651) erasing segment 12 (vno[0] = 113607) erasing segment 13 (vno[0] = 152183) erasing segment 14 (vno[0] = 152186) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->6.16) (max @ vno 151552 --> 151609) face area 0.33 +- 0.16 (0.00-->6.89) 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 10 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=62.2, 148 (148) missing vertices, mean dist 1.3 [0.0 (%0.0)->3.4 (%100.0))] %12 local maxima, %25 large gradients and %59 min vals, 515 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=21602798.0, rms=26.658 001: dt: 0.0500, sse=19110168.0, rms=25.016 (6.159%) 002: dt: 0.0500, sse=17349288.0, rms=23.788 (4.910%) 003: dt: 0.0500, sse=16009576.0, rms=22.809 (4.115%) 004: dt: 0.0500, sse=14930113.0, rms=21.988 (3.597%) 005: dt: 0.0500, sse=14025922.0, rms=21.276 (3.237%) 006: dt: 0.0500, sse=13246935.0, rms=20.644 (2.975%) 007: dt: 0.0500, sse=12561588.0, rms=20.070 (2.778%) 008: dt: 0.0500, sse=11948572.0, rms=19.543 (2.627%) 009: dt: 0.0500, sse=11393386.0, rms=19.053 (2.508%) 010: dt: 0.0500, sse=10885821.0, rms=18.593 (2.411%) positioning took 1.1 minutes mean border=61.9, 116 (80) missing vertices, mean dist 1.2 [0.1 (%0.0)->3.0 (%100.0))] %13 local maxima, %26 large gradients and %58 min vals, 478 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=11778653.0, rms=19.394 011: dt: 0.0500, sse=11305979.0, rms=18.975 (2.164%) 012: dt: 0.0500, sse=10868231.0, rms=18.577 (2.093%) 013: dt: 0.0500, sse=10461578.0, rms=18.201 (2.028%) 014: dt: 0.0500, sse=10082463.0, rms=17.842 (1.970%) 015: dt: 0.0500, sse=9728547.0, rms=17.501 (1.913%) 016: dt: 0.0500, sse=9397624.0, rms=17.175 (1.860%) 017: dt: 0.0500, sse=9087727.0, rms=16.865 (1.808%) 018: dt: 0.0500, sse=8797181.0, rms=16.568 (1.758%) 019: dt: 0.0500, sse=8524659.0, rms=16.285 (1.709%) 020: dt: 0.0500, sse=8268469.0, rms=16.014 (1.663%) positioning took 1.1 minutes mean border=61.8, 127 (58) missing vertices, mean dist 1.1 [0.1 (%0.3)->2.7 (%99.7))] %13 local maxima, %26 large gradients and %57 min vals, 467 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=8396921.0, rms=16.157 021: dt: 0.0500, sse=8152757.5, rms=15.897 (1.610%) 022: dt: 0.0500, sse=7923124.5, rms=15.648 (1.564%) 023: dt: 0.0500, sse=7706509.0, rms=15.410 (1.523%) 024: dt: 0.0500, sse=7502198.0, rms=15.181 (1.482%) 025: dt: 0.0500, sse=7309335.5, rms=14.963 (1.441%) 026: dt: 0.0500, sse=7126519.5, rms=14.752 (1.407%) 027: dt: 0.0500, sse=6952859.5, rms=14.549 (1.375%) 028: dt: 0.0500, sse=6787329.0, rms=14.353 (1.348%) 029: dt: 0.0500, sse=6629220.0, rms=14.163 (1.324%) 030: dt: 0.0500, sse=6477803.5, rms=13.979 (1.302%) positioning took 1.1 minutes mean border=61.7, 190 (47) missing vertices, mean dist 1.0 [0.1 (%3.3)->2.4 (%96.7))] %13 local maxima, %26 large gradients and %57 min vals, 430 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=6552345.0, rms=14.071 031: dt: 0.5000, sse=5456689.5, rms=12.666 (9.988%) 032: dt: 0.5000, sse=4666664.0, rms=11.540 (8.892%) 033: dt: 0.5000, sse=4065347.5, rms=10.599 (8.148%) 034: dt: 0.5000, sse=3588981.2, rms=9.786 (7.673%) 035: dt: 0.5000, sse=3191605.2, rms=9.051 (7.508%) 036: dt: 0.5000, sse=2841333.0, rms=8.349 (7.755%) 037: dt: 0.5000, sse=2517725.0, rms=7.647 (8.415%) 038: dt: 0.5000, sse=2227771.8, rms=6.959 (9.001%) 039: dt: 0.5000, sse=1980247.0, rms=6.314 (9.257%) 040: dt: 0.5000, sse=1800302.6, rms=5.800 (8.141%) 041: dt: 0.5000, sse=1672457.8, rms=5.405 (6.816%) 042: dt: 0.5000, sse=1593637.1, rms=5.145 (4.807%) 043: dt: 0.5000, sse=1543909.0, rms=4.974 (3.324%) 044: dt: 0.5000, sse=1513202.6, rms=4.865 (2.195%) 045: dt: 0.5000, sse=1489349.1, rms=4.778 (1.787%) 046: dt: 0.5000, sse=1474945.1, rms=4.726 (1.094%) rms = 4.68, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1463555.1, rms=4.682 (0.935%) 048: dt: 0.2500, sse=1407027.5, rms=4.429 (5.386%) 049: dt: 0.2500, sse=1386206.9, rms=4.348 (1.849%) rms = 4.35, time step reduction 2 of 3 to 0.125... rms = 4.32, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1379466.2, rms=4.318 (0.673%) positioning took 3.1 minutes mean border=61.4, 4348 (13) missing vertices, mean dist 0.1 [0.2 (%46.8)->0.7 (%53.2))] %21 local maxima, %21 large gradients and %52 min vals, 209 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=1580453.6, rms=4.270 051: dt: 0.5000, sse=1536655.5, rms=4.101 (3.949%) 052: dt: 0.5000, sse=1497056.2, rms=3.950 (3.684%) rms = 4.11, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1440530.8, rms=3.659 (7.380%) rms = 3.61, time step reduction 2 of 3 to 0.125... 054: dt: 0.2500, sse=1434117.4, rms=3.614 (1.228%) rms = 3.57, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1426453.2, rms=3.567 (1.293%) positioning took 1.1 minutes mean border=61.1, 4894 (10) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.5 (%55.4))] %27 local maxima, %15 large gradients and %51 min vals, 260 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=1446334.0, rms=3.677 rms = 3.95, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1433671.5, rms=3.613 (1.749%) rms = 3.66, time step reduction 2 of 3 to 0.125... rms = 3.60, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1432282.1, rms=3.605 (0.222%) positioning took 0.6 minutes mean border=60.8, 10016 (10) missing vertices, mean dist 0.1 [0.2 (%42.6)->0.4 (%57.4))] %29 local maxima, %12 large gradients and %48 min vals, 282 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-6.0.0/0050006/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1443737.0, rms=3.660 rms = 3.62, time step reduction 1 of 3 to 0.250... 058: dt: 0.5000, sse=1425259.9, rms=3.624 (0.999%) 059: dt: 0.2500, sse=1383500.9, rms=3.411 (5.874%) 060: dt: 0.2500, sse=1360999.9, rms=3.307 (3.042%) rms = 3.30, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1357993.1, rms=3.296 (0.325%) 062: dt: 0.1250, sse=1331251.2, rms=3.147 (4.524%) rms = 3.11, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1323619.4, rms=3.110 (1.195%) positioning took 1.3 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.area.pial vertex spacing 1.02 +- 0.46 (0.04-->7.47) (max @ vno 151522 --> 151599) face area 0.40 +- 0.33 (0.00-->9.88) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 152724 vertices processed 25000 of 152724 vertices processed 50000 of 152724 vertices processed 75000 of 152724 vertices processed 100000 of 152724 vertices processed 125000 of 152724 vertices processed 150000 of 152724 vertices processed 0 of 152724 vertices processed 25000 of 152724 vertices processed 50000 of 152724 vertices processed 75000 of 152724 vertices processed 100000 of 152724 vertices processed 125000 of 152724 vertices processed 150000 of 152724 vertices processed thickness calculation complete, 782:1838 truncations. 28502 vertices at 0 distance 95061 vertices at 1 distance 95383 vertices at 2 distance 47759 vertices at 3 distance 17844 vertices at 4 distance 5927 vertices at 5 distance 2002 vertices at 6 distance 679 vertices at 7 distance 308 vertices at 8 distance 146 vertices at 9 distance 71 vertices at 10 distance 58 vertices at 11 distance 55 vertices at 12 distance 42 vertices at 13 distance 38 vertices at 14 distance 36 vertices at 15 distance 36 vertices at 16 distance 11 vertices at 17 distance 22 vertices at 18 distance 15 vertices at 19 distance 19 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.thickness positioning took 16.9 minutes PIDs (15230 15233) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 04:21:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label Total face volume 308565 Total vertex volume 305456 (mask=0) #@# 0050006 lh 305456 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 04:21:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label Total face volume 306687 Total vertex volume 303030 (mask=0) #@# 0050006 rh 303030 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 04:22:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 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 = 120 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/ribbon.mgz mris_volmask took 17.74 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 04:39:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 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 0050006 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 04:39:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 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 0050006 rh pial Waiting for PID 17824 of (17824 17828 17831 17847) to complete... Waiting for PID 17828 of (17824 17828 17831 17847) to complete... Waiting for PID 17831 of (17824 17828 17831 17847) to complete... Waiting for PID 17847 of (17824 17828 17831 17847) 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 0050006 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565 Total vertex volume 305456 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1454 1006 2706 2.788 0.459 0.112 0.021 13 1.1 bankssts 920 613 1473 2.372 0.724 0.132 0.017 13 0.5 caudalanteriorcingulate 3582 2249 7632 3.081 0.553 0.118 0.033 41 4.8 caudalmiddlefrontal 2176 1436 2881 1.920 0.452 0.143 0.036 31 3.2 cuneus 718 518 2163 3.578 0.709 0.108 0.016 6 0.4 entorhinal 5367 3659 12584 2.876 0.599 0.137 0.036 85 8.2 fusiform 7839 5147 16172 2.874 0.532 0.124 0.026 91 7.9 inferiorparietal 5148 3496 13162 3.122 0.790 0.136 0.035 81 6.8 inferiortemporal 1970 1288 3747 2.535 0.895 0.128 0.024 29 1.6 isthmuscingulate 9590 5971 15819 2.438 0.634 0.132 0.033 126 12.8 lateraloccipital 4395 3043 10377 3.207 0.829 0.144 0.040 64 7.2 lateralorbitofrontal 4858 3332 8041 2.239 0.660 0.138 0.041 61 8.0 lingual 3072 2183 6075 2.633 0.811 0.164 0.053 77 6.3 medialorbitofrontal 4827 3185 12272 3.188 0.715 0.129 0.031 82 5.9 middletemporal 1055 695 2459 3.110 0.887 0.100 0.023 7 0.9 parahippocampal 2707 1696 5381 2.941 0.552 0.117 0.027 28 2.8 paracentral 2525 1712 6395 3.149 0.580 0.120 0.026 28 2.4 parsopercularis 1275 853 3948 3.336 0.741 0.135 0.031 21 1.5 parsorbitalis 2283 1529 5183 3.131 0.610 0.122 0.031 27 2.5 parstriangularis 2030 1444 2144 1.713 0.411 0.142 0.034 24 2.9 pericalcarine 7937 5066 13300 2.396 0.693 0.116 0.026 84 8.2 postcentral 1761 1210 3631 2.663 0.923 0.134 0.026 25 1.9 posteriorcingulate 9023 5814 16761 2.709 0.622 0.113 0.025 84 9.4 precentral 7345 5070 14551 2.688 0.548 0.132 0.028 99 8.9 precuneus 1058 713 1984 2.559 0.845 0.136 0.038 18 1.4 rostralanteriorcingulate 10516 6969 22103 2.861 0.551 0.128 0.028 138 11.9 rostralmiddlefrontal 12975 8588 31883 3.177 0.600 0.130 0.034 168 17.6 superiorfrontal 9630 6291 19214 2.675 0.561 0.126 0.026 113 9.6 superiorparietal 5853 3805 15174 3.283 0.819 0.106 0.022 53 5.2 superiortemporal 5800 3927 12767 2.985 0.558 0.131 0.029 81 6.5 supramarginal 496 319 1690 3.355 0.624 0.168 0.060 12 1.1 frontalpole 634 446 2892 3.935 0.810 0.158 0.060 15 1.5 temporalpole 706 436 1360 2.764 0.648 0.143 0.038 11 0.9 transversetemporal 3546 2409 7483 3.200 0.754 0.114 0.029 34 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 0050006 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565 Total vertex volume 305456 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1454 921 2706 2.788 0.459 0.116 0.031 21 2.0 bankssts 920 616 1473 2.372 0.724 0.136 0.034 29 1.3 caudalanteriorcingulate 3582 2658 7632 3.081 0.553 0.125 0.031 45 4.9 caudalmiddlefrontal 2176 1684 2881 1.920 0.452 0.143 0.038 38 3.7 cuneus 718 699 2163 3.578 0.709 0.141 0.029 15 0.9 entorhinal 5367 5034 12584 2.876 0.599 0.164 0.039 89 10.0 fusiform 7839 6032 16172 2.874 0.532 0.137 0.033 108 11.7 inferiorparietal 5148 4680 13162 3.122 0.790 0.162 0.039 76 9.7 inferiortemporal 1970 1626 3747 2.535 0.895 0.136 0.033 30 2.6 isthmuscingulate 9590 7113 15819 2.438 0.634 0.124 0.029 126 12.4 lateraloccipital 4395 3408 10377 3.207 0.829 0.149 0.041 78 8.2 lateralorbitofrontal 4858 3992 8041 2.239 0.660 0.150 0.040 63 8.8 lingual 3072 2526 6075 2.633 0.811 0.166 0.052 69 6.8 medialorbitofrontal 4827 4376 12272 3.188 0.715 0.150 0.034 65 8.0 middletemporal 1055 969 2459 3.110 0.887 0.186 0.055 24 2.7 parahippocampal 2707 2017 5381 2.941 0.552 0.136 0.037 45 4.7 paracentral 2525 2277 6395 3.149 0.580 0.155 0.034 46 4.2 parsopercularis 1275 1405 3948 3.336 0.741 0.170 0.036 16 2.1 parsorbitalis 2283 1818 5183 3.131 0.610 0.134 0.030 31 3.1 parstriangularis 2030 1124 2144 1.713 0.411 0.113 0.031 43 2.6 pericalcarine 7937 6135 13300 2.396 0.693 0.133 0.030 87 11.0 postcentral 1761 1473 3631 2.663 0.923 0.154 0.039 30 3.2 posteriorcingulate 9023 6551 16761 2.709 0.622 0.121 0.028 109 11.5 precentral 7345 5707 14551 2.688 0.548 0.136 0.032 121 10.4 precuneus 1058 854 1984 2.559 0.845 0.165 0.047 23 2.2 rostralanteriorcingulate 10516 8379 22103 2.861 0.551 0.139 0.055 286 16.6 rostralmiddlefrontal 12975 11226 31883 3.177 0.600 0.149 0.036 192 21.8 superiorfrontal 9630 7830 19214 2.675 0.561 0.138 0.033 135 14.1 superiorparietal 5853 5200 15174 3.283 0.819 0.156 0.037 81 10.7 superiortemporal 5800 4656 12767 2.985 0.558 0.143 0.032 96 8.4 supramarginal 496 677 1690 3.355 0.624 0.211 0.042 5 1.1 frontalpole 634 980 2892 3.935 0.810 0.237 0.059 40 2.2 temporalpole 706 596 1360 2.764 0.648 0.146 0.037 8 1.2 transversetemporal 3546 2200 7483 3.200 0.754 0.137 0.045 64 7.7 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 0050006 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687 Total vertex volume 303030 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1318 928 2501 2.889 0.556 0.127 0.024 12 1.4 bankssts 1443 971 2634 2.351 0.833 0.132 0.028 23 1.5 caudalanteriorcingulate 3132 2061 7122 2.979 0.516 0.108 0.024 31 2.9 caudalmiddlefrontal 2610 1683 3645 1.964 0.518 0.145 0.037 37 3.8 cuneus 686 478 2209 3.526 0.763 0.130 0.033 8 0.9 entorhinal 5428 3627 12050 2.891 0.716 0.126 0.031 75 6.6 fusiform 9662 6328 22000 2.999 0.608 0.128 0.030 125 11.1 inferiorparietal 6016 4085 15840 3.094 0.824 0.127 0.034 91 8.3 inferiortemporal 1516 998 2866 2.305 0.899 0.132 0.031 26 1.8 isthmuscingulate 9228 5735 15334 2.398 0.631 0.132 0.036 122 13.0 lateraloccipital 4357 2985 9815 3.051 0.745 0.137 0.038 62 6.4 lateralorbitofrontal 5002 3312 8038 2.250 0.604 0.149 0.048 72 10.4 lingual 3376 2259 6821 2.676 0.749 0.127 0.041 50 5.3 medialorbitofrontal 5320 3685 13994 3.083 0.709 0.125 0.026 65 5.8 middletemporal 1071 707 2045 2.609 0.697 0.108 0.025 10 1.0 parahippocampal 2915 1850 5580 2.757 0.509 0.117 0.026 28 3.1 paracentral 2480 1646 5925 3.025 0.609 0.115 0.023 26 2.3 parsopercularis 1629 1083 4369 3.306 0.636 0.143 0.032 25 2.1 parsorbitalis 2337 1604 5218 2.891 0.568 0.120 0.026 30 2.4 parstriangularis 2408 1629 2321 1.736 0.488 0.139 0.037 26 3.8 pericalcarine 6526 4051 10279 2.282 0.623 0.110 0.028 68 7.2 postcentral 2408 1651 4983 2.626 0.899 0.141 0.035 37 3.3 posteriorcingulate 7409 4656 13810 2.747 0.588 0.110 0.025 65 7.3 precentral 7797 5203 14618 2.658 0.562 0.133 0.031 106 9.2 precuneus 1067 746 2201 2.577 0.765 0.155 0.042 22 2.1 rostralanteriorcingulate 10857 7266 23821 2.877 0.586 0.129 0.030 141 13.4 rostralmiddlefrontal 12067 7918 27923 3.073 0.647 0.128 0.034 155 16.1 superiorfrontal 8917 5691 16760 2.555 0.586 0.128 0.028 112 9.7 superiorparietal 5734 3809 14467 3.204 0.746 0.113 0.025 60 5.6 superiortemporal 5625 3711 11457 2.873 0.509 0.133 0.028 79 6.4 supramarginal 560 353 1681 2.995 0.856 0.156 0.050 10 1.1 frontalpole 659 453 2651 3.771 0.837 0.127 0.037 9 1.1 temporalpole 519 346 1015 2.731 0.677 0.149 0.034 8 0.6 transversetemporal 3290 2267 7036 3.219 0.799 0.116 0.030 30 3.8 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 0050006 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687 Total vertex volume 303030 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1318 796 2501 2.889 0.556 0.130 0.037 19 2.2 bankssts 1443 1213 2634 2.351 0.833 0.145 0.035 15 2.3 caudalanteriorcingulate 3132 2605 7122 2.979 0.516 0.130 0.027 33 3.7 caudalmiddlefrontal 2610 2118 3645 1.964 0.518 0.148 0.039 39 4.7 cuneus 686 779 2209 3.526 0.763 0.173 0.042 13 1.3 entorhinal 5428 4536 12050 2.891 0.716 0.171 0.186 1579 73.6 fusiform 9662 8023 22000 2.999 0.608 0.143 0.034 133 14.9 inferiorparietal 6016 5870 15840 3.094 0.824 0.164 0.039 96 11.1 inferiortemporal 1516 1317 2866 2.305 0.899 0.144 0.032 31 2.0 isthmuscingulate 9228 6900 15334 2.398 0.631 0.128 0.061 323 34.4 lateraloccipital 4357 3518 9815 3.051 0.745 0.167 0.046 83 9.2 lateralorbitofrontal 5002 3930 8038 2.250 0.604 0.155 0.061 117 16.8 lingual 3376 2902 6821 2.676 0.749 0.166 0.047 64 7.3 medialorbitofrontal 5320 5200 13994 3.083 0.709 0.162 0.037 76 9.5 middletemporal 1071 892 2045 2.609 0.697 0.160 0.038 26 2.0 parahippocampal 2915 2142 5580 2.757 0.509 0.128 0.037 39 4.3 paracentral 2480 2283 5925 3.025 0.609 0.159 0.038 28 4.4 parsopercularis 1629 1563 4369 3.306 0.636 0.159 0.036 32 2.5 parsorbitalis 2337 2019 5218 2.891 0.568 0.157 0.035 38 4.1 parstriangularis 2408 1281 2321 1.736 0.488 0.111 0.034 52 3.3 pericalcarine 6526 5118 10279 2.282 0.623 0.132 0.031 67 9.7 postcentral 2408 2046 4983 2.626 0.899 0.149 0.036 40 4.1 posteriorcingulate 7409 5269 13810 2.747 0.588 0.119 0.028 132 9.0 precentral 7797 5807 14618 2.658 0.562 0.140 0.036 150 12.3 precuneus 1067 941 2201 2.577 0.765 0.162 0.042 14 1.9 rostralanteriorcingulate 10857 9047 23821 2.877 0.586 0.145 0.033 132 16.3 rostralmiddlefrontal 12067 9881 27923 3.073 0.647 0.148 0.039 211 21.3 superiorfrontal 8917 7124 16760 2.555 0.586 0.140 0.033 120 13.0 superiorparietal 5734 5283 14467 3.204 0.746 0.178 0.045 90 12.8 superiortemporal 5625 4274 11457 2.873 0.509 0.142 0.036 89 9.2 supramarginal 560 677 1681 2.995 0.856 0.196 0.039 6 1.2 frontalpole 659 946 2651 3.771 0.837 0.230 0.048 8 1.7 temporalpole 519 416 1015 2.731 0.677 0.161 0.051 7 1.2 transversetemporal 3290 2135 7036 3.219 0.799 0.156 0.052 69 8.3 insula PIDs (17824 17828 17831 17847) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 04:41:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 04:41:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 17957 of (17957 17960) to complete... Waiting for PID 17960 of (17957 17960) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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... 228 labels changed using aseg relabeling using gibbs priors... 000: 10087 changed, 153025 examined... 001: 2410 changed, 39255 examined... 002: 696 changed, 12466 examined... 003: 335 changed, 4014 examined... 004: 141 changed, 1897 examined... 005: 77 changed, 819 examined... 006: 43 changed, 432 examined... 007: 19 changed, 256 examined... 008: 7 changed, 110 examined... 009: 7 changed, 42 examined... 010: 0 changed, 36 examined... 7 labels changed using aseg 000: 294 total segments, 204 labels (2336 vertices) changed 001: 101 total segments, 13 labels (103 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1351 vertices marked for relabeling... 1351 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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: 9866 changed, 152724 examined... 001: 2265 changed, 38793 examined... 002: 658 changed, 11905 examined... 003: 286 changed, 3732 examined... 004: 134 changed, 1664 examined... 005: 66 changed, 751 examined... 006: 40 changed, 388 examined... 007: 20 changed, 229 examined... 008: 15 changed, 121 examined... 009: 7 changed, 84 examined... 010: 5 changed, 44 examined... 011: 1 changed, 29 examined... 012: 0 changed, 9 examined... 12 labels changed using aseg 000: 293 total segments, 205 labels (2677 vertices) changed 001: 103 total segments, 16 labels (56 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1098 vertices marked for relabeling... 1098 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. PIDs (17957 17960) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 04:41:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 04:41:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh white Waiting for PID 18053 of (18053 18056) to complete... Waiting for PID 18056 of (18053 18056) 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 0050006 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565 Total vertex volume 305456 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1663 1104 3745 2.952 0.731 0.138 0.036 23 2.4 G&S_frontomargin 2203 1451 4556 2.787 0.521 0.136 0.031 33 2.8 G&S_occipital_inf 2099 1266 3859 2.574 0.635 0.114 0.031 22 2.5 G&S_paracentral 1755 1145 4019 3.178 0.588 0.127 0.028 22 1.7 G&S_subcentral 941 615 2696 3.142 0.573 0.157 0.039 20 1.4 G&S_transv_frontopol 2124 1498 4490 3.002 0.547 0.134 0.031 27 2.5 G&S_cingul-Ant 1437 1044 2928 2.989 0.545 0.115 0.019 10 1.1 G&S_cingul-Mid-Ant 1283 906 2916 3.186 0.611 0.122 0.025 10 1.3 G&S_cingul-Mid-Post 788 526 2231 3.166 0.636 0.145 0.034 15 0.9 G_cingul-Post-dorsal 347 216 849 2.963 0.809 0.154 0.032 7 0.3 G_cingul-Post-ventral 2060 1329 2781 1.894 0.446 0.148 0.039 32 3.4 G_cuneus 1504 1001 4107 3.031 0.634 0.125 0.032 23 1.8 G_front_inf-Opercular 561 354 1763 3.252 0.747 0.161 0.047 14 0.8 G_front_inf-Orbital 1464 949 3903 3.174 0.652 0.137 0.039 23 2.2 G_front_inf-Triangul 5418 3385 13257 3.021 0.566 0.137 0.038 97 8.1 G_front_middle 9502 6062 25496 3.248 0.636 0.139 0.040 150 15.4 G_front_sup 601 425 1512 3.136 0.911 0.127 0.044 9 0.9 G_Ins_lg&S_cent_ins 713 441 2106 3.480 0.996 0.113 0.028 9 0.8 G_insular_short 2936 1733 6611 2.832 0.563 0.137 0.033 46 3.7 G_occipital_middle 1827 1141 3113 2.323 0.616 0.148 0.035 28 2.4 G_occipital_sup 2283 1505 5526 2.912 0.605 0.150 0.045 49 4.2 G_oc-temp_lat-fusifor 3405 2249 5693 2.169 0.657 0.159 0.050 55 7.2 G_oc-temp_med-Lingual 1700 1113 4741 3.389 0.773 0.120 0.030 21 1.7 G_oc-temp_med-Parahip 2764 1823 7966 3.199 0.909 0.149 0.046 52 5.1 G_orbital 2904 1836 7188 3.016 0.580 0.134 0.033 47 3.5 G_pariet_inf-Angular 3013 2017 7340 2.950 0.633 0.148 0.037 59 4.7 G_pariet_inf-Supramar 3768 2429 9113 2.861 0.580 0.139 0.033 59 4.5 G_parietal_sup 3148 1878 5284 2.303 0.479 0.123 0.030 39 3.8 G_postcentral 3403 2042 7017 2.788 0.676 0.120 0.031 41 4.6 G_precentral 3514 2350 8693 2.851 0.570 0.139 0.033 63 4.8 G_precuneus 991 717 2536 2.791 0.817 0.185 0.067 34 2.4 G_rectus 875 602 1235 2.170 1.034 0.166 0.070 25 2.6 G_subcallosal 529 303 1106 2.774 0.733 0.130 0.041 9 0.7 G_temp_sup-G_T_transv 2003 1263 7404 3.603 0.815 0.130 0.027 30 2.2 G_temp_sup-Lateral 656 455 1950 3.818 0.764 0.091 0.020 3 0.6 G_temp_sup-Plan_polar 932 636 2070 2.845 0.785 0.092 0.016 7 0.4 G_temp_sup-Plan_tempo 2628 1721 7403 3.145 0.875 0.148 0.044 55 4.4 G_temporal_inf 2896 1868 8610 3.290 0.706 0.140 0.038 66 4.2 G_temporal_middle 322 232 604 3.036 0.383 0.114 0.012 2 0.2 Lat_Fis-ant-Horizont 235 159 379 2.714 0.545 0.092 0.018 1 0.1 Lat_Fis-ant-Vertical 1220 830 1779 2.815 0.554 0.134 0.029 13 1.4 Lat_Fis-post 2544 1476 3226 2.028 0.625 0.140 0.042 39 4.2 Pole_occipital 1614 1152 6283 3.625 0.727 0.152 0.051 33 3.2 Pole_temporal 2775 2031 3651 2.123 0.739 0.133 0.029 30 3.8 S_calcarine 3248 2233 3965 2.032 0.564 0.109 0.019 22 2.6 S_central 1197 836 1885 2.595 0.400 0.097 0.012 6 0.6 S_cingul-Marginalis 642 443 1116 3.164 0.586 0.093 0.014 2 0.4 S_circular_insula_ant 1517 1025 2755 3.298 0.614 0.093 0.018 8 1.2 S_circular_insula_inf 1748 1228 3089 3.117 0.515 0.099 0.016 7 1.2 S_circular_insula_sup 1269 897 2327 2.968 0.528 0.100 0.014 7 0.8 S_collat_transv_ant 545 365 718 2.248 0.448 0.143 0.039 6 0.9 S_collat_transv_post 2588 1769 4781 2.940 0.504 0.106 0.017 18 1.9 S_front_inf 2320 1572 3831 2.642 0.507 0.115 0.022 20 2.3 S_front_middle 2924 1987 5682 2.890 0.416 0.110 0.021 23 2.6 S_front_sup 73 55 183 3.556 0.395 0.188 0.044 1 0.1 S_interm_prim-Jensen 2758 1877 4478 2.630 0.393 0.104 0.017 18 1.8 S_intrapariet&P_trans 1442 969 1956 2.365 0.449 0.115 0.024 10 1.5 S_oc_middle&Lunatus 1545 1041 2293 2.356 0.453 0.112 0.019 12 1.2 S_oc_sup&transversal 781 553 1574 2.852 0.462 0.122 0.024 8 0.8 S_occipital_ant 818 591 1302 2.471 0.412 0.124 0.022 8 0.8 S_oc-temp_lat 2007 1441 3798 2.640 0.711 0.107 0.021 13 1.7 S_oc-temp_med&Lingual 569 385 937 2.920 0.515 0.083 0.011 2 0.2 S_orbital_lateral 582 534 1223 2.695 0.761 0.167 0.030 7 0.8 S_orbital_med-olfact 1789 1234 4003 3.410 0.643 0.133 0.033 20 2.3 S_orbital-H_Shaped 2523 1725 4082 2.437 0.541 0.118 0.023 25 2.4 S_parieto_occipital 1450 891 1086 1.557 0.474 0.131 0.020 27 0.8 S_pericallosal 4406 2988 7717 2.738 0.506 0.105 0.020 31 3.3 S_postcentral 1826 1225 3337 3.008 0.513 0.114 0.022 14 1.6 S_precentral-inf-part 1939 1321 3416 2.836 0.440 0.106 0.018 14 1.3 S_precentral-sup-part 751 513 1223 2.754 0.510 0.123 0.025 9 0.8 S_suborbital 1783 1266 2809 2.508 0.455 0.127 0.023 16 1.8 S_subparietal 1618 1160 3178 3.084 0.603 0.119 0.021 12 1.5 S_temporal_inf 6723 4499 12376 2.884 0.553 0.110 0.020 52 5.5 S_temporal_sup 354 236 602 2.994 0.613 0.110 0.016 2 0.3 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 0050006 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687 Total vertex volume 303030 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1186 791 2713 2.721 0.854 0.139 0.040 16 1.8 G&S_frontomargin 1580 1044 2817 2.451 0.662 0.119 0.026 19 1.6 G&S_occipital_inf 1858 1102 3397 2.577 0.607 0.118 0.036 22 2.6 G&S_paracentral 1528 1002 3115 2.689 0.619 0.142 0.041 25 2.7 G&S_subcentral 1328 889 3530 3.010 0.593 0.156 0.039 24 2.3 G&S_transv_frontopol 3239 2265 6843 2.903 0.566 0.123 0.030 38 4.2 G&S_cingul-Ant 1741 1191 3489 2.879 0.569 0.126 0.031 21 2.0 G&S_cingul-Mid-Ant 1687 1171 3685 2.968 0.568 0.123 0.029 16 1.9 G&S_cingul-Mid-Post 708 470 2150 3.049 0.693 0.161 0.053 16 1.7 G_cingul-Post-dorsal 351 214 773 2.687 0.668 0.139 0.036 6 0.4 G_cingul-Post-ventral 2437 1562 3475 1.941 0.579 0.146 0.038 36 4.0 G_cuneus 1859 1215 4487 2.842 0.621 0.127 0.028 25 2.0 G_front_inf-Opercular 479 307 1301 2.993 0.732 0.165 0.044 12 0.8 G_front_inf-Orbital 931 638 2653 3.053 0.491 0.136 0.034 18 1.4 G_front_inf-Triangul 4936 3093 13520 3.095 0.541 0.143 0.039 97 7.4 G_front_middle 8102 5139 20966 3.149 0.717 0.139 0.040 134 13.1 G_front_sup 634 426 1652 3.501 0.815 0.126 0.035 9 0.8 G_Ins_lg&S_cent_ins 757 497 1923 3.317 1.017 0.121 0.039 9 1.1 G_insular_short 3633 2210 8815 2.961 0.584 0.140 0.038 59 5.1 G_occipital_middle 2096 1320 3832 2.339 0.716 0.149 0.034 32 3.1 G_occipital_sup 2091 1361 5552 2.992 0.737 0.144 0.038 40 3.3 G_oc-temp_lat-fusifor 3200 2025 5175 2.144 0.614 0.152 0.049 50 6.7 G_oc-temp_med-Lingual 1679 1119 4442 3.131 0.827 0.137 0.044 26 2.9 G_oc-temp_med-Parahip 3365 2265 9470 3.246 0.740 0.146 0.039 62 5.0 G_orbital 3548 2236 10113 3.232 0.658 0.145 0.039 65 5.1 G_pariet_inf-Angular 2859 1858 6802 3.031 0.523 0.138 0.032 48 3.6 G_pariet_inf-Supramar 2916 1775 6680 2.742 0.595 0.138 0.035 49 3.8 G_parietal_sup 2500 1369 4123 2.309 0.567 0.108 0.035 31 3.4 G_postcentral 2571 1415 5648 2.908 0.558 0.105 0.029 27 2.8 G_precentral 3160 2065 7359 2.763 0.579 0.148 0.038 60 4.7 G_precuneus 864 588 2299 2.647 0.737 0.152 0.055 19 2.1 G_rectus 574 358 714 2.184 0.841 0.133 0.063 12 1.2 G_subcallosal 370 253 876 2.654 0.706 0.147 0.034 6 0.5 G_temp_sup-G_T_transv 2128 1383 6899 3.437 0.733 0.139 0.034 35 2.9 G_temp_sup-Lateral 848 563 2525 3.660 0.767 0.107 0.031 8 0.9 G_temp_sup-Plan_polar 766 522 1651 2.724 0.692 0.107 0.024 8 0.6 G_temp_sup-Plan_tempo 3287 2220 10301 3.292 0.851 0.144 0.041 63 5.7 G_temporal_inf 3145 2143 9978 3.274 0.759 0.142 0.035 55 4.5 G_temporal_middle 382 272 582 2.741 0.587 0.107 0.014 2 0.2 Lat_Fis-ant-Horizont 261 181 454 2.752 0.402 0.091 0.022 1 0.2 Lat_Fis-ant-Vertical 1172 854 1986 2.847 0.431 0.120 0.020 8 0.9 Lat_Fis-post 4152 2419 5712 2.115 0.588 0.142 0.048 61 7.8 Pole_occipital 1673 1127 5899 3.554 0.801 0.143 0.039 29 2.7 Pole_temporal 2788 1962 3488 2.092 0.604 0.145 0.040 35 4.9 S_calcarine 2768 1877 3208 1.989 0.505 0.094 0.016 12 1.8 S_central 1500 1024 2685 2.649 0.555 0.126 0.024 15 1.6 S_cingul-Marginalis 766 532 1258 3.093 0.619 0.107 0.019 4 0.7 S_circular_insula_ant 1143 770 1988 2.964 0.694 0.082 0.012 4 0.6 S_circular_insula_inf 1487 1022 2491 3.069 0.596 0.100 0.018 7 1.1 S_circular_insula_sup 1623 1088 2756 2.718 0.525 0.091 0.019 12 1.2 S_collat_transv_ant 429 293 631 2.296 0.422 0.137 0.033 4 0.6 S_collat_transv_post 2665 1822 5390 2.885 0.577 0.105 0.019 18 2.0 S_front_inf 2700 1893 4449 2.667 0.476 0.112 0.021 17 2.4 S_front_middle 3286 2248 6365 2.889 0.450 0.108 0.023 22 3.0 S_front_sup 437 301 651 2.733 0.360 0.131 0.020 4 0.4 S_interm_prim-Jensen 3253 2181 5228 2.470 0.474 0.107 0.017 24 2.2 S_intrapariet&P_trans 1098 781 1431 2.303 0.406 0.125 0.028 8 1.3 S_oc_middle&Lunatus 1273 897 1954 2.425 0.384 0.113 0.018 9 0.9 S_oc_sup&transversal 885 614 1672 2.725 0.447 0.105 0.016 6 0.6 S_occipital_ant 1532 1070 2728 2.905 0.695 0.100 0.021 11 1.2 S_oc-temp_lat 1939 1353 3198 2.574 0.636 0.112 0.021 14 1.6 S_oc-temp_med&Lingual 445 317 698 2.709 0.479 0.113 0.015 3 0.3 S_orbital_lateral 836 573 1289 2.535 0.776 0.130 0.034 9 1.1 S_orbital_med-olfact 1703 1154 3624 3.106 0.635 0.124 0.031 16 2.1 S_orbital-H_Shaped 2944 1990 4302 2.491 0.597 0.123 0.024 30 2.6 S_parieto_occipital 1915 1222 1410 1.544 0.449 0.119 0.017 27 1.0 S_pericallosal 3067 2047 4447 2.511 0.394 0.116 0.021 27 2.4 S_postcentral 1447 998 2927 2.957 0.582 0.100 0.015 8 0.9 S_precentral-inf-part 1639 1137 2872 2.844 0.470 0.105 0.018 10 1.2 S_precentral-sup-part 465 318 800 2.769 0.634 0.109 0.022 3 0.4 S_suborbital 1780 1215 2995 2.664 0.483 0.116 0.024 14 1.4 S_subparietal 1482 1050 2508 2.514 0.547 0.105 0.016 10 1.1 S_temporal_inf 7166 4883 12789 2.896 0.517 0.113 0.022 59 6.5 S_temporal_sup 286 200 422 2.941 0.412 0.133 0.022 2 0.2 S_temporal_transverse PIDs (18053 18056) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 04:42:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 04:42:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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 18112 of (18112 18115) to complete... Waiting for PID 18115 of (18112 18115) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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... 1759 labels changed using aseg relabeling using gibbs priors... 000: 2116 changed, 153025 examined... 001: 496 changed, 9886 examined... 002: 143 changed, 2884 examined... 003: 52 changed, 855 examined... 004: 23 changed, 310 examined... 005: 8 changed, 124 examined... 006: 8 changed, 59 examined... 007: 7 changed, 43 examined... 008: 6 changed, 36 examined... 009: 4 changed, 33 examined... 010: 7 changed, 26 examined... 011: 5 changed, 34 examined... 012: 7 changed, 28 examined... 013: 3 changed, 34 examined... 014: 4 changed, 21 examined... 015: 3 changed, 17 examined... 016: 4 changed, 17 examined... 017: 6 changed, 28 examined... 018: 4 changed, 28 examined... 019: 4 changed, 23 examined... 020: 3 changed, 26 examined... 021: 3 changed, 18 examined... 022: 2 changed, 17 examined... 023: 4 changed, 13 examined... 024: 3 changed, 21 examined... 025: 4 changed, 21 examined... 026: 3 changed, 23 examined... 027: 2 changed, 22 examined... 028: 1 changed, 12 examined... 029: 1 changed, 7 examined... 030: 1 changed, 7 examined... 031: 2 changed, 7 examined... 032: 1 changed, 10 examined... 033: 1 changed, 7 examined... 034: 3 changed, 7 examined... 035: 5 changed, 13 examined... 036: 1 changed, 17 examined... 037: 3 changed, 8 examined... 038: 3 changed, 14 examined... 039: 0 changed, 14 examined... 291 labels changed using aseg 000: 63 total segments, 30 labels (320 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1041 vertices marked for relabeling... 1041 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050006 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... 1595 labels changed using aseg relabeling using gibbs priors... 000: 2132 changed, 152724 examined... 001: 525 changed, 9901 examined... 002: 148 changed, 3016 examined... 003: 72 changed, 899 examined... 004: 37 changed, 419 examined... 005: 26 changed, 219 examined... 006: 25 changed, 142 examined... 007: 22 changed, 125 examined... 008: 12 changed, 102 examined... 009: 7 changed, 67 examined... 010: 5 changed, 42 examined... 011: 5 changed, 29 examined... 012: 2 changed, 29 examined... 013: 2 changed, 16 examined... 014: 1 changed, 11 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 1 changed, 7 examined... 018: 1 changed, 7 examined... 019: 2 changed, 9 examined... 020: 1 changed, 14 examined... 021: 0 changed, 7 examined... 245 labels changed using aseg 000: 58 total segments, 25 labels (212 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 8 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 987 vertices marked for relabeling... 987 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. PIDs (18112 18115) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 04:42:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 04:42:39 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh white Waiting for PID 18177 of (18177 18180) to complete... Waiting for PID 18180 of (18177 18180) 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 0050006 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 308565 Total vertex volume 305456 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1847 1270 3891 2.762 0.749 0.132 0.022 25 1.5 caudalanteriorcingulate 3894 2466 8232 3.063 0.543 0.119 0.033 45 5.1 caudalmiddlefrontal 3079 2025 4282 2.004 0.475 0.133 0.033 41 4.1 cuneus 690 483 2064 3.570 0.685 0.111 0.023 8 0.6 entorhinal 4965 3384 11141 2.839 0.588 0.134 0.032 75 7.0 fusiform 7673 5021 15958 2.873 0.538 0.124 0.026 89 7.8 inferiorparietal 5230 3550 13403 3.096 0.791 0.137 0.037 84 7.5 inferiortemporal 1911 1253 3699 2.580 0.890 0.129 0.024 28 1.6 isthmuscingulate 9593 5967 15829 2.438 0.631 0.132 0.032 126 12.4 lateraloccipital 5009 3463 11972 3.105 0.946 0.152 0.046 83 9.7 lateralorbitofrontal 5046 3447 8243 2.224 0.656 0.140 0.041 64 8.5 lingual 2303 1669 5142 2.707 0.783 0.164 0.056 64 4.7 medialorbitofrontal 6414 4298 15772 3.154 0.671 0.128 0.030 100 7.5 middletemporal 1084 711 2487 3.124 0.894 0.098 0.022 7 0.8 parahippocampal 3297 2070 6843 3.015 0.551 0.118 0.029 34 3.6 paracentral 2281 1530 5707 3.146 0.603 0.123 0.028 27 2.3 parsopercularis 1297 873 3415 3.110 0.684 0.135 0.028 20 1.3 parsorbitalis 2890 1950 6199 3.072 0.573 0.117 0.027 30 3.0 parstriangularis 1972 1409 2087 1.711 0.408 0.143 0.034 23 2.9 pericalcarine 9055 5804 15247 2.437 0.688 0.116 0.026 94 9.3 postcentral 1955 1347 3855 2.669 0.898 0.130 0.026 25 2.0 posteriorcingulate 8743 5625 16312 2.721 0.625 0.113 0.025 80 8.9 precentral 7305 5023 14742 2.714 0.541 0.135 0.029 103 9.0 precuneus 1498 1043 2696 2.708 0.719 0.134 0.032 21 1.7 rostralanteriorcingulate 7675 5033 16912 2.947 0.561 0.127 0.028 102 8.6 rostralmiddlefrontal 14128 9318 33795 3.092 0.625 0.132 0.034 192 19.6 superiorfrontal 7674 5029 15658 2.713 0.554 0.126 0.026 90 7.6 superiorparietal 7462 4934 20065 3.273 0.832 0.111 0.025 77 7.6 superiortemporal 5448 3697 11953 2.980 0.565 0.132 0.029 78 6.1 supramarginal 721 449 1368 2.744 0.633 0.146 0.038 12 1.0 transversetemporal 2944 1990 6490 3.267 0.735 0.107 0.026 26 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 0050006 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 306687 Total vertex volume 303030 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1578 1058 2805 2.338 0.829 0.131 0.028 24 1.7 caudalanteriorcingulate 3395 2230 7527 2.975 0.506 0.110 0.024 34 3.1 caudalmiddlefrontal 3332 2125 4701 2.028 0.535 0.141 0.035 46 4.8 cuneus 620 439 2096 3.610 0.778 0.127 0.033 7 0.7 entorhinal 4984 3348 10648 2.840 0.685 0.126 0.031 68 6.1 fusiform 9550 6244 21562 2.989 0.609 0.129 0.030 125 11.0 inferiorparietal 6455 4371 17078 3.106 0.830 0.125 0.033 94 8.5 inferiortemporal 1454 960 2792 2.344 0.888 0.134 0.031 25 1.7 isthmuscingulate 9194 5706 15241 2.396 0.629 0.133 0.036 122 13.1 lateraloccipital 4948 3371 11685 3.029 0.788 0.137 0.039 72 7.4 lateralorbitofrontal 4888 3237 7870 2.243 0.602 0.149 0.047 70 10.0 lingual 2425 1632 5224 2.652 0.769 0.138 0.047 42 4.5 medialorbitofrontal 6540 4512 16526 3.049 0.683 0.126 0.026 80 7.1 middletemporal 1131 757 2215 2.650 0.708 0.108 0.024 11 1.0 parahippocampal 3007 1920 5860 2.764 0.517 0.116 0.026 27 3.1 paracentral 2802 1863 6771 3.045 0.607 0.115 0.024 29 2.6 parsopercularis 1459 972 3505 3.080 0.739 0.135 0.031 20 1.7 parsorbitalis 2325 1586 5083 2.914 0.562 0.123 0.026 30 2.5 parstriangularis 2356 1604 2301 1.741 0.491 0.138 0.036 24 3.7 pericalcarine 7293 4545 11654 2.307 0.634 0.111 0.029 78 8.3 postcentral 2453 1680 5033 2.637 0.892 0.140 0.035 37 3.3 posteriorcingulate 7171 4467 13519 2.751 0.596 0.111 0.026 65 7.3 precentral 7887 5271 14959 2.668 0.565 0.135 0.032 110 9.5 precuneus 1388 952 2655 2.537 0.743 0.142 0.040 25 2.4 rostralanteriorcingulate 7494 5033 16261 2.892 0.584 0.128 0.029 94 8.9 rostralmiddlefrontal 15822 10417 36372 3.037 0.627 0.130 0.033 209 21.2 superiorfrontal 7288 4644 13768 2.561 0.570 0.127 0.027 92 7.6 superiorparietal 7339 4931 18947 3.231 0.762 0.119 0.028 82 8.5 superiortemporal 5300 3497 10954 2.888 0.513 0.132 0.028 74 5.9 supramarginal 506 342 1025 2.722 0.663 0.146 0.033 8 0.6 transversetemporal 2944 2031 6393 3.229 0.823 0.110 0.025 25 2.8 insula PIDs (18177 18180) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 04:43:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts pctsurfcon --s 0050006 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 04:43:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts pctsurfcon --s 0050006 --rh-only Waiting for PID 18235 of (18235 18246) to complete... Waiting for PID 18246 of (18235 18246) to complete... pctsurfcon --s 0050006 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts/pctsurfcon.log Sun Oct 8 04:43:22 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-6.0.0/0050006/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-573 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-6.0.0/0050006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.wm.mgh --regheader 0050006 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00003; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 76909 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.wm.mgh Dim: 153025 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.gm.mgh --projfrac 0.3 --regheader 0050006 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00003; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 92775 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.gm.mgh Dim: 153025 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18235/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.w-g.pct.mgh --annot 0050006 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/lh.w-g.pct.mgh --annot 0050006 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-573 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/lh.w-g.pct.mgh Vertex Area is 0.66309 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 0050006 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/scripts/pctsurfcon.log Sun Oct 8 04:43:22 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-6.0.0/0050006/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-573 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-6.0.0/0050006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.wm.mgh --regheader 0050006 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00003; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 76245 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.wm.mgh Dim: 152724 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.gm.mgh --projfrac 0.3 --regheader 0050006 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00003; 0.00000 -1.00000 0.00000 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 92814 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.gm.mgh Dim: 152724 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/tmp.pctsurfcon.18246/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.w-g.pct.mgh --annot 0050006 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.w-g.pct.mgh --annot 0050006 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-573 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.w-g.pct.mgh Vertex Area is 0.659549 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 (18235 18246) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 04:43:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2112 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2058 voxels changed to hypointensity... 4100 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 04:43:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 mri_aparc2aseg --s 0050006 --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 04:43:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 mri_aparc2aseg --s 0050006 --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 04:43:54 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 mri_aparc2aseg --s 0050006 --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 18468 of (18468 18471 18474) to complete... Waiting for PID 18471 of (18468 18471 18474) to complete... Waiting for PID 18474 of (18468 18471 18474) to complete... mri_aparc2aseg --s 0050006 --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 0050006 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/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 7.11 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 65 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 85 rescaling Left_Pallidum from 98 --> 94 rescaling Third_Ventricle from 25 --> 33 rescaling Fourth_Ventricle from 22 --> 20 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 65 rescaling Left_Amygdala from 56 --> 68 rescaling CSF from 32 --> 46 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 65 rescaling Right_Lateral_Ventricle from 13 --> 18 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 92 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 67 rescaling Right_Accumbens_area from 65 --> 73 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 40 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 76 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 = 602800 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 230 changed. pass 2: 40 changed. pass 3: 18 changed. pass 4: 11 changed. pass 5: 7 changed. pass 6: 1 changed. pass 7: 1 changed. pass 8: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050006 --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 0050006 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/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 7.11 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 65 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 85 rescaling Left_Pallidum from 98 --> 94 rescaling Third_Ventricle from 25 --> 33 rescaling Fourth_Ventricle from 22 --> 20 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 65 rescaling Left_Amygdala from 56 --> 68 rescaling CSF from 32 --> 46 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 65 rescaling Right_Lateral_Ventricle from 13 --> 18 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 92 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 67 rescaling Right_Accumbens_area from 65 --> 73 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 40 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 76 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 = 602783 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 230 changed. pass 2: 40 changed. pass 3: 18 changed. pass 4: 11 changed. pass 5: 7 changed. pass 6: 1 changed. pass 7: 1 changed. pass 8: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050006 --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 0050006 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/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-6.0.0/0050006/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 7.11 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 65 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 35 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 86 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 85 rescaling Left_Pallidum from 98 --> 94 rescaling Third_Ventricle from 25 --> 33 rescaling Fourth_Ventricle from 22 --> 20 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 65 rescaling Left_Amygdala from 56 --> 68 rescaling CSF from 32 --> 46 rescaling Left_Accumbens_area from 62 --> 64 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 65 rescaling Right_Lateral_Ventricle from 13 --> 18 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 92 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 86 rescaling Right_Caudate from 62 --> 75 rescaling Right_Putamen from 80 --> 79 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 67 rescaling Right_Accumbens_area from 65 --> 73 rescaling Right_VentralDC from 86 --> 96 rescaling Fifth_Ventricle from 40 --> 40 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 76 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 = 602783 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 230 changed. pass 2: 40 changed. pass 3: 18 changed. pass 4: 11 changed. pass 5: 7 changed. pass 6: 1 changed. pass 7: 1 changed. pass 8: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (18468 18471 18474) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 04:53:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 04:53:45 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-6.0.0/0050006/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-573 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-6.0.0/0050006/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-573 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 04:53:45 CEST 2017 Ended at Sun Oct 8 04:53:51 CEST 2017 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 04:53:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 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 0050006 $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 0050006 sysname Linux hostname tars-573 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1616394 mm^3 (det: 1.205217 ) Computing euler number orig.nofix lheno = -108, rheno = -92 orig.nofix lhholes = 55, rhholes = 47 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 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 04:55:37 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006 mri_aparc2aseg --s 0050006 --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 0050006 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-6.0.0/0050006/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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-6.0.0/0050006/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7954 vertices from left hemi Ripped 7355 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-6.0.0/0050006/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 = 1071593 Used brute-force search on 111 voxels Fixing Parahip LH WM Found 12 clusters 0 k 48.000000 1 k 1.000000 2 k 4.000000 3 k 1.000000 4 k 3.000000 5 k 2.000000 6 k 1.000000 7 k 1616.000000 8 k 1.000000 9 k 1.000000 10 k 3.000000 11 k 1.000000 Fixing Parahip RH WM Found 6 clusters 0 k 2.000000 1 k 1524.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 40.000000 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 0050006 --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 0050006 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-573 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1616394 mm^3 (det: 1.205217 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 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-6.0.0/0050006/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 05:05:12 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 19709 of (19709 19715 19721 19727 19732) to complete... Waiting for PID 19715 of (19709 19715 19721 19727 19732) to complete... Waiting for PID 19721 of (19709 19715 19721 19727 19732) to complete... Waiting for PID 19727 of (19709 19715 19721 19727 19732) to complete... Waiting for PID 19732 of (19709 19715 19721 19727 19732) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 704 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4833 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 1460 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9369 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 191 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4268 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 527 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6510 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 1028 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6812 mri_label2label: Done PIDs (19709 19715 19721 19727 19732) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 19788 of (19788 19794 19800 19806) to complete... Waiting for PID 19794 of (19788 19794 19800 19806) to complete... Waiting for PID 19800 of (19788 19794 19800 19806) to complete... Waiting for PID 19806 of (19788 19794 19800 19806) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4417 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 2733 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 16322 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 403 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4584 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 1198 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4620 mri_label2label: Done PIDs (19788 19794 19800 19806) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 19853 of (19853 19859 19865 19870 19877) to complete... Waiting for PID 19859 of (19853 19859 19865 19870 19877) to complete... Waiting for PID 19865 of (19853 19859 19865 19870 19877) to complete... Waiting for PID 19870 of (19853 19859 19865 19870 19877) to complete... Waiting for PID 19877 of (19853 19859 19865 19870 19877) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 1467 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6108 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 3588 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11702 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 775 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2793 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1493 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 239 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1438 mri_label2label: Done PIDs (19853 19859 19865 19870 19877) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 19939 of (19939 19945 19951 19957 19962) to complete... Waiting for PID 19945 of (19939 19945 19951 19957 19962) to complete... Waiting for PID 19951 of (19939 19945 19951 19957 19962) to complete... Waiting for PID 19957 of (19939 19945 19951 19957 19962) to complete... Waiting for PID 19962 of (19939 19945 19951 19957 19962) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1235 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 556 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2648 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1581 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 143 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2139 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 413 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2732 mri_label2label: Done PIDs (19939 19945 19951 19957 19962) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 20135 of (20135 20141 20147 20152) to complete... Waiting for PID 20141 of (20135 20141 20147 20152) to complete... Waiting for PID 20147 of (20135 20141 20147 20152) to complete... Waiting for PID 20152 of (20135 20141 20147 20152) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1620 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 1432 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8467 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2045 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 434 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1585 mri_label2label: Done PIDs (20135 20141 20147 20152) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 20198 of (20198 20204 20210 20215 20220) to complete... Waiting for PID 20204 of (20198 20204 20210 20215 20220) to complete... Waiting for PID 20210 of (20198 20204 20210 20215 20220) to complete... Waiting for PID 20215 of (20198 20204 20210 20215 20220) to complete... Waiting for PID 20220 of (20198 20204 20210 20215 20220) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 918 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4323 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 1704 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5038 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 698 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 531 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 153025 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 576 mri_label2label: Done PIDs (20198 20204 20210 20215 20220) completed and logs appended. mris_label2annot --s 0050006 --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-6.0.0/0050006/label cmdline mris_label2annot --s 0050006 --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-573 machine x86_64 user ntraut subject 0050006 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-6.0.0/0050006/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 103255 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/lh.BA_exvivo.annot mris_label2annot --s 0050006 --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-6.0.0/0050006/label cmdline mris_label2annot --s 0050006 --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-573 machine x86_64 user ntraut subject 0050006 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-6.0.0/0050006/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 123872 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 308565 Total vertex volume 305456 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1525 844 2689 2.421 0.426 0.117 0.033 18 1.9 BA1_exvivo 5656 3767 10294 2.686 0.514 0.110 0.022 49 4.6 BA2_exvivo 1147 764 1109 1.904 0.473 0.139 0.027 11 1.3 BA3a_exvivo 2552 1712 4158 2.152 0.854 0.119 0.026 27 2.6 BA3b_exvivo 2183 1296 4188 2.792 0.532 0.113 0.030 21 2.8 BA4a_exvivo 1321 935 2101 2.354 0.546 0.103 0.022 6 1.2 BA4p_exvivo 12206 7771 27084 3.030 0.620 0.123 0.033 158 16.6 BA6_exvivo 2354 1592 5385 3.113 0.531 0.115 0.026 24 2.4 BA44_exvivo 3756 2516 8391 3.023 0.642 0.121 0.027 42 3.8 BA45_exvivo 3539 2474 4047 1.684 0.436 0.139 0.036 42 5.3 V1_exvivo 9429 5993 13981 2.223 0.589 0.147 0.041 139 16.1 V2_exvivo 2530 1653 5387 2.947 0.483 0.129 0.027 33 2.7 MT_exvivo 656 463 1925 3.696 0.671 0.098 0.014 4 0.4 perirhinal_exvivo 916 612 3060 3.499 0.682 0.131 0.031 15 1.3 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 0050006 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 308565 Total vertex volume 305456 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1005 533 1760 2.399 0.454 0.125 0.037 14 1.3 BA1_exvivo 2335 1570 4114 2.502 0.440 0.115 0.025 22 2.3 BA2_exvivo 997 662 898 1.839 0.413 0.142 0.030 10 1.2 BA3a_exvivo 1538 1035 1888 1.743 0.456 0.109 0.021 14 1.3 BA3b_exvivo 2076 1273 3792 2.669 0.566 0.113 0.031 19 2.7 BA4a_exvivo 1098 762 1694 2.411 0.526 0.100 0.020 5 1.0 BA4p_exvivo 7153 4494 15395 2.978 0.595 0.122 0.033 95 10.0 BA6_exvivo 1448 983 3502 3.084 0.552 0.123 0.029 18 1.6 BA44_exvivo 1455 945 4021 3.245 0.621 0.134 0.032 21 1.8 BA45_exvivo 3751 2616 4464 1.720 0.481 0.138 0.037 45 5.5 V1_exvivo 4767 2959 6654 2.134 0.563 0.152 0.045 77 9.1 V2_exvivo 655 434 1365 2.951 0.433 0.130 0.024 7 0.6 MT_exvivo 348 255 914 3.696 0.657 0.095 0.011 2 0.2 perirhinal_exvivo 527 336 1552 3.545 0.720 0.122 0.031 9 0.6 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 05:08:46 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 20355 of (20355 20361 20367 20373 20377) to complete... Waiting for PID 20361 of (20355 20361 20367 20373 20377) to complete... Waiting for PID 20367 of (20355 20361 20367 20373 20377) to complete... Waiting for PID 20373 of (20355 20361 20367 20373 20377) to complete... Waiting for PID 20377 of (20355 20361 20367 20373 20377) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 431 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4393 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 640 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7327 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4066 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4777 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 600 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6347 mri_label2label: Done PIDs (20355 20361 20367 20373 20377) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 20428 of (20428 20434 20440 20444) to complete... Waiting for PID 20434 of (20428 20434 20440 20444) to complete... Waiting for PID 20440 of (20428 20434 20440 20444) to complete... Waiting for PID 20444 of (20428 20434 20440 20444) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 235 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4708 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 1353 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13609 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 1102 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8014 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 1516 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6871 mri_label2label: Done PIDs (20428 20434 20440 20444) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 20502 of (20502 20508 20514 20519 20524) to complete... Waiting for PID 20508 of (20502 20508 20514 20519 20524) to complete... Waiting for PID 20514 of (20502 20508 20514 20519 20524) to complete... Waiting for PID 20519 of (20502 20508 20514 20519 20524) to complete... Waiting for PID 20524 of (20502 20508 20514 20519 20524) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 2029 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6756 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 3717 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11733 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 870 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2802 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1245 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 913 mri_label2label: Done PIDs (20502 20508 20514 20519 20524) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 20635 of (20635 20641 20647 20652 20658) to complete... Waiting for PID 20641 of (20635 20641 20647 20652 20658) to complete... Waiting for PID 20647 of (20635 20641 20647 20652 20658) to complete... Waiting for PID 20652 of (20635 20641 20647 20652 20658) to complete... Waiting for PID 20658 of (20635 20641 20647 20652 20658) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 155 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1031 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2886 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1727 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2254 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1601 mri_label2label: Done PIDs (20635 20641 20647 20652 20658) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 20719 of (20719 20725 20731 20737) to complete... Waiting for PID 20725 of (20719 20725 20731 20737) to complete... Waiting for PID 20731 of (20719 20725 20731 20737) to complete... Waiting for PID 20737 of (20719 20725 20731 20737) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1541 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 704 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7663 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 300 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1312 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1362 mri_label2label: Done PIDs (20719 20725 20731 20737) 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 0050006 --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 0050006 --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 0050006 --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 0050006 --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 0050006 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 20777 of (20777 20783 20789 20794 20800) to complete... Waiting for PID 20783 of (20777 20783 20789 20794 20800) to complete... Waiting for PID 20789 of (20777 20783 20789 20794 20800) to complete... Waiting for PID 20794 of (20777 20783 20789 20794 20800) to complete... Waiting for PID 20800 of (20777 20783 20789 20794 20800) 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 1279 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4511 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 1676 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5113 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 418 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 833 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 0050006 --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 = 0050006 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-6.0.0/0050006/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 152724 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 350 mri_label2label: Done PIDs (20777 20783 20789 20794 20800) completed and logs appended. mris_label2annot --s 0050006 --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-6.0.0/0050006/label cmdline mris_label2annot --s 0050006 --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-573 machine x86_64 user ntraut subject 0050006 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-6.0.0/0050006/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 106878 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/label/rh.BA_exvivo.annot mris_label2annot --s 0050006 --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-6.0.0/0050006/label cmdline mris_label2annot --s 0050006 --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-573 machine x86_64 user ntraut subject 0050006 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-6.0.0/0050006/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 127337 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/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 0050006 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 306687 Total vertex volume 303030 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 1111 571 1987 2.437 0.582 0.126 0.039 18 1.5 BA1_exvivo 3661 2337 5774 2.492 0.465 0.113 0.026 36 3.8 BA2_exvivo 1039 693 1016 1.902 0.454 0.127 0.025 9 1.0 BA3a_exvivo 1840 1190 2629 1.936 0.592 0.094 0.023 14 1.8 BA3b_exvivo 1868 1093 3570 2.772 0.468 0.106 0.025 15 1.9 BA4a_exvivo 1168 774 1813 2.395 0.482 0.090 0.018 5 0.8 BA4p_exvivo 8745 5506 19425 3.022 0.628 0.119 0.032 105 11.5 BA6_exvivo 4082 2720 8966 2.925 0.599 0.118 0.025 41 4.1 BA44_exvivo 4779 3224 11370 2.987 0.620 0.126 0.026 60 5.0 BA45_exvivo 4367 2785 5288 1.905 0.560 0.136 0.045 53 8.1 V1_exvivo 9320 5891 13554 2.152 0.584 0.148 0.042 139 16.2 V2_exvivo 2696 1785 5263 2.736 0.535 0.118 0.025 27 2.5 MT_exvivo 718 480 2171 3.403 0.724 0.133 0.035 10 1.0 perirhinal_exvivo 452 319 1360 3.254 0.852 0.114 0.025 6 0.4 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 0050006 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050006/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 306687 Total vertex volume 303030 (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) = 1616394 mm^3 (det: 1.205217 ) lhCtxGM: 303019.103 302203.000 diff= 816.1 pctdiff= 0.269 rhCtxGM: 300790.957 300235.000 diff= 556.0 pctdiff= 0.185 lhCtxWM: 237481.483 238242.000 diff= -760.5 pctdiff=-0.320 rhCtxWM: 233553.125 234089.000 diff= -535.9 pctdiff=-0.229 SubCortGMVol 63577.000 SupraTentVol 1150941.667 (1147430.000) diff=3511.667 pctdiff=0.305 SupraTentVolNotVent 1141857.667 (1138346.000) diff=3511.667 pctdiff=0.308 BrainSegVol 1317564.000 (1316137.000) diff=1427.000 pctdiff=0.108 BrainSegVolNotVent 1305905.000 (1305911.667) diff=-6.667 pctdiff=-0.001 BrainSegVolNotVent 1305905.000 CerebellumVol 167490.000 VentChorVol 9084.000 3rd4th5thCSF 2575.000 CSFVol 1148.000, OptChiasmVol 69.000 MaskVol 1699011.000 771 381 1287 2.315 0.599 0.134 0.054 15 1.6 BA1_exvivo 2004 1255 3290 2.466 0.434 0.098 0.019 16 1.5 BA2_exvivo 914 613 785 1.838 0.361 0.134 0.025 8 0.9 BA3a_exvivo 1415 951 1679 1.720 0.373 0.075 0.014 5 0.8 BA3b_exvivo 1238 712 2394 2.796 0.454 0.112 0.031 13 1.5 BA4a_exvivo 977 649 1403 2.327 0.454 0.088 0.018 3 0.7 BA4p_exvivo 5637 3529 12484 3.041 0.549 0.115 0.029 61 6.0 BA6_exvivo 1189 799 3119 3.007 0.634 0.118 0.025 14 1.1 BA44_exvivo 1112 754 3000 3.008 0.476 0.122 0.030 15 1.4 BA45_exvivo 4169 2686 4904 1.869 0.539 0.137 0.044 50 7.7 V1_exvivo 4804 3001 6563 2.043 0.517 0.154 0.047 79 9.3 V2_exvivo 408 248 975 3.037 0.547 0.120 0.028 4 0.4 MT_exvivo 432 290 1218 3.324 0.712 0.124 0.031 5 0.6 perirhinal_exvivo 317 236 844 3.389 0.756 0.101 0.018 2 0.2 entorhinal_exvivo Started at Sat Oct 7 18:13:09 CEST 2017 Ended at Sun Oct 8 05:12:19 CEST 2017 #@#%# recon-all-run-time-hours 10.986 recon-all -s 0050006 finished without error at Sun Oct 8 05:12:19 CEST 2017