Sun Oct 8 01:37:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050566 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050566/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050566 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-604 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 53756420 12237428 1741464 0 49932056 -/+ buffers/cache: 3824364 62169484 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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: 2017/10/07-23:37:07-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-604 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-6.0.0/0050566 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050566/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050566/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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/Yale/0050566/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-6.0.0/0050566/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Oct 8 01:37:12 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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 float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Oct 8 01:37:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-604 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 Sun Oct 8 01:37:21 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.24582 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24582/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24582/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.24582/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Oct 8 01:37:24 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.24582/nu0.mnc ./tmp.mri_nu_correct.mni.24582/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24582/0/ -iterations 1000 -distance 50 [ntraut@tars-604:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/] [2017-10-08 01:37:24] 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.24582/0/ ./tmp.mri_nu_correct.mni.24582/nu0.mnc ./tmp.mri_nu_correct.mni.24582/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 54 CV of field change: 0.000992525 mri_convert ./tmp.mri_nu_correct.mni.24582/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.24582/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.24582/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... Sun Oct 8 01:38:38 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 Sun Oct 8 01:38:38 CEST 2017 Ended at Sun Oct 8 01:39:09 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Oct 8 01:39:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6856, pval=0.4932 >= 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-6.0.0/0050566/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach_avi.log TalAviQA: 0.97932 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sun Oct 8 01:39:11 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-6.0.0/0050566/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-604 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 Sun Oct 8 01:39:12 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.25515 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25515/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25515/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.25515/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Oct 8 01:39:14 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.25515/nu0.mnc ./tmp.mri_nu_correct.mni.25515/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25515/0/ [ntraut@tars-604:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/] [2017-10-08 01:39:14] 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.25515/0/ ./tmp.mri_nu_correct.mni.25515/nu0.mnc ./tmp.mri_nu_correct.mni.25515/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 39 CV of field change: 0.000961806 -------------------------------------------------------- Iteration 2 Sun Oct 8 01:40:02 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.25515/nu1.mnc ./tmp.mri_nu_correct.mni.25515/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25515/1/ [ntraut@tars-604:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/] [2017-10-08 01:40:02] 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.25515/1/ ./tmp.mri_nu_correct.mni.25515/nu1.mnc ./tmp.mri_nu_correct.mni.25515/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 Number of iterations: 22 CV of field change: 0.000970114 mri_binarize --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25515/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-6.0.0/0050566/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25515/ones.mgz sysname Linux hostname tars-604 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.25515/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.25515/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.25515/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/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.25515/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/input.mean.dat sysname Linux hostname tars-604 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.25515/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.25515/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25515/ones.mgz --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/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.25515/ones.mgz --i ./tmp.mri_nu_correct.mni.25515/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25515/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25515/output.mean.dat sysname Linux hostname tars-604 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.25515/ones.mgz Loading ./tmp.mri_nu_correct.mni.25515/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.25515/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.25515/nu2.mnc ./tmp.mri_nu_correct.mni.25515/nu2.mnc mul 1.01812367956321046405 Saving result to './tmp.mri_nu_correct.mni.25515/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.25515/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.25515/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.25515/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 ( 5, 116) to ( 3, 110) Sun Oct 8 01:41:14 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sun Oct 8 01:41:14 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 1.12323 0.05093 -0.02905 -43.66782; -0.02742 1.01447 0.40186 50.74092; -0.01426 -0.33404 1.08284 -13.44376; 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 = 14 Starting OpenSpline(): npoints = 14 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 55 (55), valley at 19 (19) csf peak at 28, setting threshold to 46 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 58 (58), valley at 18 (18) csf peak at 30, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 57 seconds. #-------------------------------------------- #@# Skull Stripping Sun Oct 8 01:43:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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=11.0 skull bounding box = (51, 76, 23) --> (200, 226, 209) using (101, 126, 116) as brain centroid... mean wm in atlas = 108, using box (83,108,93) --> (119, 144,138) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 4.9 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.698 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.364028 @ (9.091, -27.273, -9.091) max log p = -4.318834 @ (-4.545, -4.545, -4.545) max log p = -4.265907 @ (-6.818, 2.273, 2.273) max log p = -4.261907 @ (1.136, 1.136, 1.136) max log p = -4.246409 @ (0.568, -0.568, 0.568) max log p = -4.235481 @ (0.284, -0.284, -0.284) Found translation: (-0.3, -29.3, -9.9): log p = -4.235 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.842, old_max_log_p =-4.235 (thresh=-4.2) 1.15000 0.00000 0.00000 -19.05799; 0.00000 1.11081 0.29764 -76.73383; 0.00000 -0.27532 1.02750 33.93199; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.842, old_max_log_p =-3.842 (thresh=-3.8) 1.15000 0.00000 0.00000 -19.05799; 0.00000 1.11081 0.29764 -76.73383; 0.00000 -0.27532 1.02750 33.93199; 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=-3.776, old_max_log_p =-3.842 (thresh=-3.8) 1.12783 0.01157 -0.03350 -14.20147; 0.00000 1.09043 0.36421 -81.30061; 0.03692 -0.35346 1.02344 44.57402; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.775, old_max_log_p =-3.776 (thresh=-3.8) 1.14898 0.01179 -0.03413 -16.80915; -0.00121 1.10141 0.33053 -79.01006; 0.03759 -0.32355 1.05421 35.91718; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.747, old_max_log_p =-3.775 (thresh=-3.8) 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.747, old_max_log_p =-3.747 (thresh=-3.7) 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 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 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.747 (old=-4.698) transform before final EM align: 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 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 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.15029 0.00281 -0.03710 -15.13517; 0.00843 1.09493 0.33766 -79.51074; 0.03762 -0.33138 1.04777 38.43645; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1244.197853 mri_em_register stimesec 1.343795 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 157061 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 336 mri_em_register ru_nivcsw 17717 registration took 10 minutes and 51 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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=127 y=143 z=111 r=65 first estimation of the main basin volume: 1151627 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=146, y=135, z=80, Imax=255 CSF=18, 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=8110681402 voxels, voxel volume =1.000 = 8110681402 mmm3 = 8110681.600 cm3 done. PostAnalyze...Basin Prior 13 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=125,y=148, z=106, r=9451 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=23, CSF_MAX=58 , nb = 44074 RIGHT_CER CSF_MIN=0, CSF_intensity=23, CSF_MAX=56 , nb = -1029927675 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=86 , nb = -1031222087 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=52 , nb = 1110004096 LEFT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=66 , nb = 1061772250 OTHER CSF_MIN=11, CSF_intensity=25, CSF_MAX=55 , nb = 1082347322 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 58, 43, 36, 55 after analyzing : 37, 43, 43, 46 RIGHT_CER before analyzing : 56, 48, 43, 67 after analyzing : 41, 48, 48, 52 LEFT_CER before analyzing : 86, 50, 42, 61 after analyzing : 38, 50, 50, 52 RIGHT_BRAIN before analyzing : 52, 41, 34, 55 after analyzing : 36, 41, 41, 44 LEFT_BRAIN before analyzing : 66, 45, 37, 56 after analyzing : 39, 45, 45, 47 OTHER before analyzing : 55, 58, 62, 94 after analyzing : 55, 60, 62, 68 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 68.119, std = 7.127 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.57, sigma = 5.56 after rotation: sse = 3.57, sigma = 5.56 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.02, its var is 6.23 before Erosion-Dilatation 1.18% 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...36 iterations mri_strip_skull: done peeling brain Brain Size = 1528172 voxels, voxel volume = 1.000 mm3 = 1528172 mmm3 = 1528.172 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 26.829921 mri_watershed stimesec 0.531919 mri_watershed ru_maxrss 818064 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211644 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 4456 mri_watershed ru_oublock 2424 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 2012 mri_watershed ru_nivcsw 174 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Oct 8 01:54:29 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 2 == reading 1 input volumes... logging results to talairach.log reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (60, 85, 32) --> (187, 226, 193) using (102, 132, 113) as brain centroid... mean wm in atlas = 107, using box (86,115,93) --> (117, 149,132) 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 1.000 scaling channel 0 by 1 initial log_p = -4.386 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.023443 @ (9.091, -27.273, -9.091) max log p = -3.926755 @ (-4.545, -4.545, 4.545) max log p = -3.823371 @ (-2.273, 2.273, -6.818) max log p = -3.811545 @ (-1.136, 1.136, 3.409) max log p = -3.787865 @ (0.568, -0.568, -0.568) max log p = -3.787865 @ (0.000, 0.000, 0.000) Found translation: (1.7, -29.0, -8.5): log p = -3.788 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.510, old_max_log_p =-3.788 (thresh=-3.8) 1.06375 0.00000 0.00000 -6.26628; 0.00000 1.06753 0.42117 -79.48959; 0.00000 -0.43171 0.98772 64.38564; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.510, old_max_log_p =-3.510 (thresh=-3.5) 1.06375 0.00000 0.00000 -6.26628; 0.00000 1.06753 0.42117 -79.48959; 0.00000 -0.43171 0.98772 64.38564; 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=-3.315, old_max_log_p =-3.510 (thresh=-3.5) 1.08085 -0.05724 -0.05528 4.05277; 0.06734 1.06185 0.30742 -78.89843; 0.03276 -0.31854 1.00387 40.20407; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.315, old_max_log_p =-3.315 (thresh=-3.3) 1.08085 -0.05724 -0.05528 4.05277; 0.06734 1.06185 0.30742 -78.89843; 0.03276 -0.31854 1.00387 40.20407; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.280, old_max_log_p =-3.315 (thresh=-3.3) 1.07959 -0.05717 -0.05522 4.66420; 0.06763 1.05279 0.32267 -78.30307; 0.03170 -0.33626 0.99987 44.31944; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.275, old_max_log_p =-3.280 (thresh=-3.3) 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.275, old_max_log_p =-3.275 (thresh=-3.3) 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 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 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.275 (old=-4.386) transform before final EM align: 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 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 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.8 after pass:transform: ( 1.08, -0.06, -0.06, 4.52) ( 0.07, 1.05, 0.32, -78.07) ( 0.03, -0.34, 1.00, 44.39) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1291.609645 mri_em_register stimesec 1.575760 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 158956 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 376 mri_em_register ru_nivcsw 18249 registration took 11 minutes and 14 seconds. #-------------------------------------- #@# CA Normalize Sun Oct 8 02:05:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (60, 85, 32) --> (187, 226, 193) using (102, 132, 113) as brain centroid... mean wm in atlas = 107, using box (86,115,93) --> (117, 149,132) 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 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.08085 -0.05724 -0.05528 4.52115; 0.06755 1.05155 0.32229 -78.07096; 0.03166 -0.33587 0.99870 44.39106; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 86, 35) --> (188, 195, 191) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 4977 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 87, 35) --> (128, 189, 192) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 4956 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 172, 65) --> (174, 209, 117) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 194 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 172, 64) --> (127, 210, 118) Right_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0 0 of 36 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 157, 98) --> (145, 221, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 142 (0.0%) samples deleted using 10305 total control points for intensity normalization... bias field = 0.963 +- 0.048 102 of 10305 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 86, 35) --> (188, 195, 191) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 5291 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 87, 35) --> (128, 189, 192) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 5483 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 172, 65) --> (174, 209, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 307 (8.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 172, 64) --> (127, 210, 118) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 76 (1.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 157, 98) --> (145, 221, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 84 of 265 (31.7%) samples deleted using 11422 total control points for intensity normalization... bias field = 1.029 +- 0.044 34 of 11239 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 86, 35) --> (188, 195, 191) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 5330 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 87, 35) --> (128, 189, 192) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 2 of 5436 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 172, 65) --> (174, 209, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 80 of 317 (25.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (87, 172, 64) --> (127, 210, 118) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 96 (25.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 157, 98) --> (145, 221, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 153 of 270 (56.7%) samples deleted using 11449 total control points for intensity normalization... bias field = 1.028 +- 0.038 14 of 10994 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 41 seconds. #-------------------------------------- #@# CA Reg Sun Oct 8 02:07:24 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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) = 1.26 (predicted orig area = 6.4) 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=0.801, neg=0, invalid=762 0001: dt=231.608392, rms=0.720 (10.159%), neg=0, invalid=762 0002: dt=144.972376, rms=0.698 (2.959%), neg=0, invalid=762 0003: dt=254.645503, rms=0.687 (1.598%), neg=0, invalid=762 0004: dt=131.742690, rms=0.681 (0.874%), neg=0, invalid=762 0005: dt=369.920000, rms=0.676 (0.775%), neg=0, invalid=762 0006: dt=110.976000, rms=0.672 (0.586%), neg=0, invalid=762 0007: dt=517.888000, rms=0.668 (0.636%), neg=0, invalid=762 0008: dt=129.472000, rms=0.666 (0.303%), neg=0, invalid=762 0009: dt=295.936000, rms=0.664 (0.220%), neg=0, invalid=762 0010: dt=295.936000, rms=0.664 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0011: dt=129.472000, rms=0.662 (0.371%), neg=0, invalid=762 0012: dt=517.888000, rms=0.660 (0.299%), neg=0, invalid=762 0013: dt=129.472000, rms=0.659 (0.170%), neg=0, invalid=762 0014: dt=129.472000, rms=0.659 (0.073%), neg=0, invalid=762 0015: dt=129.472000, rms=0.658 (0.134%), neg=0, invalid=762 0016: dt=129.472000, rms=0.657 (0.190%), neg=0, invalid=762 0017: dt=129.472000, rms=0.655 (0.212%), neg=0, invalid=762 0018: dt=129.472000, rms=0.654 (0.222%), neg=0, invalid=762 0019: dt=129.472000, rms=0.652 (0.229%), neg=0, invalid=762 0020: dt=129.472000, rms=0.651 (0.232%), neg=0, invalid=762 0021: dt=129.472000, rms=0.649 (0.233%), neg=0, invalid=762 0022: dt=129.472000, rms=0.648 (0.219%), neg=0, invalid=762 0023: dt=129.472000, rms=0.647 (0.196%), neg=0, invalid=762 0024: dt=129.472000, rms=0.645 (0.182%), neg=0, invalid=762 0025: dt=129.472000, rms=0.644 (0.171%), neg=0, invalid=762 0026: dt=129.472000, rms=0.643 (0.156%), neg=0, invalid=762 0027: dt=129.472000, rms=0.642 (0.139%), neg=0, invalid=762 0028: dt=129.472000, rms=0.642 (0.123%), neg=0, invalid=762 0029: dt=129.472000, rms=0.641 (0.105%), neg=0, invalid=762 0030: dt=517.888000, rms=0.641 (0.052%), neg=0, invalid=762 0031: dt=517.888000, rms=0.641 (-0.219%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0032: dt=117.870504, rms=0.638 (0.998%), neg=0, invalid=762 0033: dt=110.625430, rms=0.631 (1.093%), neg=0, invalid=762 0034: dt=77.217391, rms=0.628 (0.508%), neg=0, invalid=762 0035: dt=108.178478, rms=0.624 (0.700%), neg=0, invalid=762 0036: dt=80.516129, rms=0.622 (0.338%), neg=0, invalid=762 0037: dt=95.255814, rms=0.618 (0.569%), neg=0, invalid=762 0038: dt=36.288000, rms=0.617 (0.224%), neg=0, invalid=762 0039: dt=36.288000, rms=0.616 (0.119%), neg=0, invalid=762 0040: dt=36.288000, rms=0.615 (0.221%), neg=0, invalid=762 0041: dt=36.288000, rms=0.613 (0.325%), neg=0, invalid=762 0042: dt=36.288000, rms=0.610 (0.404%), neg=0, invalid=762 0043: dt=36.288000, rms=0.608 (0.435%), neg=0, invalid=762 0044: dt=36.288000, rms=0.605 (0.434%), neg=0, invalid=762 0045: dt=36.288000, rms=0.602 (0.417%), neg=0, invalid=762 0046: dt=36.288000, rms=0.600 (0.378%), neg=0, invalid=762 0047: dt=36.288000, rms=0.598 (0.353%), neg=0, invalid=762 0048: dt=36.288000, rms=0.596 (0.326%), neg=0, invalid=762 0049: dt=36.288000, rms=0.594 (0.285%), neg=0, invalid=762 0050: dt=36.288000, rms=0.593 (0.255%), neg=0, invalid=762 0051: dt=36.288000, rms=0.591 (0.236%), neg=0, invalid=762 0052: dt=36.288000, rms=0.590 (0.223%), neg=0, invalid=762 0053: dt=36.288000, rms=0.589 (0.196%), neg=0, invalid=762 0054: dt=36.288000, rms=0.588 (0.177%), neg=0, invalid=762 0055: dt=36.288000, rms=0.587 (0.160%), neg=0, invalid=762 0056: dt=36.288000, rms=0.586 (0.128%), neg=0, invalid=762 0057: dt=36.288000, rms=0.586 (0.123%), neg=0, invalid=762 0058: dt=36.288000, rms=0.585 (0.115%), neg=0, invalid=762 0059: dt=414.720000, rms=0.584 (0.132%), neg=0, invalid=762 0060: dt=36.288000, rms=0.584 (0.046%), neg=0, invalid=762 0061: dt=36.288000, rms=0.584 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.585, neg=0, invalid=762 0062: dt=36.288000, rms=0.583 (0.212%), neg=0, invalid=762 0063: dt=36.288000, rms=0.583 (0.031%), neg=0, invalid=762 0064: dt=36.288000, rms=0.583 (0.021%), neg=0, invalid=762 0065: dt=36.288000, rms=0.583 (0.026%), neg=0, invalid=762 0066: dt=36.288000, rms=0.583 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0067: dt=8.000000, rms=0.604 (0.193%), neg=0, invalid=762 0068: dt=2.800000, rms=0.603 (0.012%), neg=0, invalid=762 0069: dt=2.800000, rms=0.603 (0.002%), neg=0, invalid=762 0070: dt=2.800000, rms=0.603 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.604, neg=0, invalid=762 0071: dt=0.000000, rms=0.603 (0.116%), neg=0, invalid=762 0072: dt=0.000000, rms=0.603 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.659, neg=0, invalid=762 0073: dt=5.510730, rms=0.645 (2.152%), neg=0, invalid=762 0074: dt=2.561798, rms=0.644 (0.076%), neg=0, invalid=762 0075: dt=2.561798, rms=0.644 (-0.027%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0076: dt=0.000000, rms=0.644 (0.093%), neg=0, invalid=762 0077: dt=0.000000, rms=0.644 (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=0.702, neg=0, invalid=762 0078: dt=0.804124, rms=0.700 (0.333%), neg=0, invalid=762 0079: dt=1.792000, rms=0.697 (0.401%), neg=0, invalid=762 0080: dt=1.792000, rms=0.695 (0.323%), neg=0, invalid=762 0081: dt=1.280000, rms=0.694 (0.063%), neg=0, invalid=762 0082: dt=1.280000, rms=0.694 (0.019%), neg=0, invalid=762 0083: dt=1.280000, rms=0.694 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0084: dt=1.536000, rms=0.693 (0.251%), neg=0, invalid=762 0085: dt=0.000000, rms=0.693 (0.001%), neg=0, invalid=762 0086: dt=0.100000, rms=0.693 (-0.005%), 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=0.651, neg=0, invalid=762 0087: dt=0.836683, rms=0.633 (2.678%), neg=0, invalid=762 0088: dt=0.080000, rms=0.632 (0.152%), neg=0, invalid=762 0089: dt=0.080000, rms=0.632 (-0.081%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0090: dt=0.028000, rms=0.632 (0.113%), neg=0, invalid=762 0091: dt=0.000063, rms=0.632 (0.001%), neg=0, invalid=762 0092: dt=0.000063, rms=0.632 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.09608 (12) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (779 voxels, overlap=0.359) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (779 voxels, peak = 11), gca=10.9 gca peak = 0.15565 (16) mri peak = 0.04813 (12) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (771 voxels, overlap=0.610) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (771 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06036 (88) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (815 voxels, overlap=0.995) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (815 voxels, peak = 88), gca=87.8 gca peak = 0.20183 (93) mri peak = 0.07597 (94) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (763 voxels, overlap=0.926) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (763 voxels, peak = 90), gca=89.7 gca peak = 0.21683 (55) mri peak = 0.09189 (60) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (607 voxels, overlap=0.992) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (607 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.08633 (58) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (866 voxels, overlap=0.998) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (866 voxels, peak = 58), gca=58.0 gca peak = 0.11430 (101) mri peak = 0.08703 (102) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57357 voxels, overlap=0.748) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (57357 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.09979 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (58063 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (58063 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03769 (55) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (29446 voxels, overlap=0.970) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (29446 voxels, peak = 56), gca=55.8 gca peak = 0.15082 (58) mri peak = 0.04026 (53) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (29163 voxels, overlap=0.950) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (29163 voxels, peak = 53), gca=53.1 gca peak = 0.14161 (67) mri peak = 0.08816 (67) Right_Caudate (50): linear fit = 0.98 x + 0.0 (861 voxels, overlap=0.900) Right_Caudate (50): linear fit = 0.98 x + 0.0 (861 voxels, peak = 65), gca=65.3 gca peak = 0.15243 (71) mri peak = 0.12715 (68) Left_Caudate (11): linear fit = 0.93 x + 0.0 (951 voxels, overlap=0.539) Left_Caudate (11): linear fit = 0.93 x + 0.0 (951 voxels, peak = 66), gca=65.7 gca peak = 0.13336 (57) mri peak = 0.04892 (56) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (33034 voxels, overlap=0.990) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (33034 voxels, peak = 56), gca=56.1 gca peak = 0.13252 (56) mri peak = 0.05006 (55) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (32983 voxels, overlap=0.964) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (32983 voxels, peak = 56), gca=55.7 gca peak = 0.18181 (84) mri peak = 0.07121 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8874 voxels, overlap=0.633) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8874 voxels, peak = 90), gca=90.3 gca peak = 0.20573 (83) mri peak = 0.05254 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7463 voxels, overlap=0.457) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7463 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.10245 (58) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (410 voxels, peak = 58), gca=58.4 gca peak = 0.39313 (56) mri peak = 0.14683 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (505 voxels, overlap=0.984) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (505 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05595 (82) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5177 voxels, overlap=0.985) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5177 voxels, peak = 83), gca=82.9 gca peak = 0.11978 (83) mri peak = 0.06415 (83) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4175 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4175 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.06234 (75) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2325 voxels, overlap=1.000) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2325 voxels, peak = 78), gca=77.8 gca peak = 0.14159 (79) mri peak = 0.06107 (72) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2196 voxels, overlap=0.923) Right_Putamen (51): linear fit = 0.94 x + 0.0 (2196 voxels, peak = 74), gca=73.9 gca peak = 0.10025 (80) mri peak = 0.08218 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12046 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12046 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06335 (92) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1003 voxels, overlap=0.728) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1003 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.06764 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1354 voxels, overlap=0.626) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1354 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 1.00000 (50) gca peak = 0.15061 (21) mri peak = 0.07757 (12) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (337 voxels, overlap=0.602) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (337 voxels, peak = 15), gca=14.8 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 1.00 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.92 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=0.655, neg=0, invalid=762 0093: dt=170.007722, rms=0.646 (1.288%), neg=0, invalid=762 0094: dt=129.472000, rms=0.644 (0.335%), neg=0, invalid=762 0095: dt=295.936000, rms=0.641 (0.463%), neg=0, invalid=762 0096: dt=92.480000, rms=0.640 (0.199%), neg=0, invalid=762 0097: dt=517.888000, rms=0.637 (0.447%), neg=0, invalid=762 0098: dt=73.984000, rms=0.636 (0.075%), neg=0, invalid=762 0099: dt=517.888000, rms=0.635 (0.187%), neg=0, invalid=762 0100: dt=129.472000, rms=0.634 (0.135%), neg=0, invalid=762 0101: dt=110.976000, rms=0.634 (0.020%), neg=0, invalid=762 0102: dt=110.976000, rms=0.634 (0.058%), neg=0, invalid=762 0103: dt=110.976000, rms=0.633 (0.079%), neg=0, invalid=762 0104: dt=110.976000, rms=0.633 (0.091%), neg=0, invalid=762 0105: dt=110.976000, rms=0.632 (0.112%), neg=0, invalid=762 0106: dt=110.976000, rms=0.631 (0.120%), neg=0, invalid=762 0107: dt=110.976000, rms=0.631 (0.123%), neg=0, invalid=762 0108: dt=110.976000, rms=0.630 (0.108%), neg=0, invalid=762 0109: dt=110.976000, rms=0.629 (0.091%), neg=0, invalid=762 0110: dt=110.976000, rms=0.629 (0.083%), neg=0, invalid=762 0111: dt=110.976000, rms=0.628 (0.076%), neg=0, invalid=762 0112: dt=110.976000, rms=0.628 (0.074%), neg=0, invalid=762 0113: dt=110.976000, rms=0.627 (0.065%), neg=0, invalid=762 0114: dt=110.976000, rms=0.627 (0.061%), neg=0, invalid=762 0115: dt=110.976000, rms=0.627 (0.061%), neg=0, invalid=762 0116: dt=110.976000, rms=0.626 (0.057%), neg=0, invalid=762 0117: dt=110.976000, rms=0.626 (0.051%), neg=0, invalid=762 0118: dt=110.976000, rms=0.626 (0.048%), neg=0, invalid=762 0119: dt=110.976000, rms=0.625 (0.047%), neg=0, invalid=762 0120: dt=110.976000, rms=0.625 (0.045%), neg=0, invalid=762 0121: dt=110.976000, rms=0.625 (0.046%), neg=0, invalid=762 0122: dt=110.976000, rms=0.625 (0.043%), neg=0, invalid=762 0123: dt=110.976000, rms=0.624 (0.051%), neg=0, invalid=762 0124: dt=110.976000, rms=0.624 (0.054%), neg=0, invalid=762 0125: dt=110.976000, rms=0.624 (0.050%), neg=0, invalid=762 0126: dt=110.976000, rms=0.623 (0.046%), neg=0, invalid=762 0127: dt=110.976000, rms=0.623 (0.044%), neg=0, invalid=762 0128: dt=110.976000, rms=0.623 (0.042%), neg=0, invalid=762 0129: dt=110.976000, rms=0.623 (0.040%), neg=0, invalid=762 0130: dt=110.976000, rms=0.622 (0.039%), neg=0, invalid=762 0131: dt=110.976000, rms=0.622 (0.039%), neg=0, invalid=762 0132: dt=110.976000, rms=0.622 (0.036%), neg=0, invalid=762 0133: dt=110.976000, rms=0.622 (0.035%), neg=0, invalid=762 0134: dt=110.976000, rms=0.621 (0.039%), neg=0, invalid=762 0135: dt=110.976000, rms=0.621 (0.032%), neg=0, invalid=762 0136: dt=110.976000, rms=0.621 (0.027%), neg=0, invalid=762 0137: dt=110.976000, rms=0.621 (0.030%), neg=0, invalid=762 0138: dt=110.976000, rms=0.621 (0.027%), neg=0, invalid=762 0139: dt=110.976000, rms=0.620 (0.032%), neg=0, invalid=762 0140: dt=110.976000, rms=0.620 (0.026%), neg=0, invalid=762 0141: dt=110.976000, rms=0.620 (0.026%), neg=0, invalid=762 0142: dt=110.976000, rms=0.620 (0.020%), neg=0, invalid=762 0143: dt=110.976000, rms=0.620 (0.022%), neg=0, invalid=762 0144: dt=110.976000, rms=0.620 (0.018%), neg=0, invalid=762 0145: dt=517.888000, rms=0.620 (0.008%), neg=0, invalid=762 0146: dt=517.888000, rms=0.620 (-0.091%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.620, neg=0, invalid=762 0147: dt=129.472000, rms=0.619 (0.220%), neg=0, invalid=762 0148: dt=369.920000, rms=0.619 (0.070%), neg=0, invalid=762 0149: dt=129.472000, rms=0.618 (0.025%), neg=0, invalid=762 0150: dt=129.472000, rms=0.618 (0.017%), neg=0, invalid=762 0151: dt=129.472000, rms=0.618 (0.025%), neg=0, invalid=762 0152: dt=129.472000, rms=0.618 (0.030%), neg=0, invalid=762 0153: dt=129.472000, rms=0.618 (0.027%), neg=0, invalid=762 0154: dt=129.472000, rms=0.618 (0.027%), neg=0, invalid=762 0155: dt=129.472000, rms=0.618 (0.028%), neg=0, invalid=762 0156: dt=129.472000, rms=0.617 (0.028%), neg=0, invalid=762 0157: dt=129.472000, rms=0.617 (0.031%), neg=0, invalid=762 0158: dt=129.472000, rms=0.617 (0.027%), neg=0, invalid=762 0159: dt=129.472000, rms=0.617 (0.023%), neg=0, invalid=762 0160: dt=129.472000, rms=0.617 (0.024%), neg=0, invalid=762 0161: dt=129.472000, rms=0.617 (0.020%), neg=0, invalid=762 0162: dt=295.936000, rms=0.617 (0.004%), neg=0, invalid=762 0163: dt=295.936000, rms=0.616 (0.016%), neg=0, invalid=762 0164: dt=295.936000, rms=0.616 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.618, neg=0, invalid=762 0165: dt=103.680000, rms=0.614 (0.645%), neg=0, invalid=762 0166: dt=132.266667, rms=0.609 (0.789%), neg=0, invalid=762 0167: dt=52.413793, rms=0.607 (0.376%), neg=0, invalid=762 0168: dt=145.152000, rms=0.603 (0.617%), neg=0, invalid=762 0169: dt=36.288000, rms=0.602 (0.187%), neg=0, invalid=762 0170: dt=580.608000, rms=0.594 (1.362%), neg=0, invalid=762 0171: dt=36.288000, rms=0.592 (0.344%), neg=0, invalid=762 0172: dt=145.152000, rms=0.590 (0.248%), neg=0, invalid=762 0173: dt=62.208000, rms=0.589 (0.117%), neg=0, invalid=762 0174: dt=145.152000, rms=0.588 (0.230%), neg=0, invalid=762 0175: dt=36.288000, rms=0.587 (0.098%), neg=0, invalid=762 0176: dt=580.608000, rms=0.584 (0.574%), neg=0, invalid=762 0177: dt=36.288000, rms=0.583 (0.263%), neg=0, invalid=762 0178: dt=331.776000, rms=0.581 (0.255%), neg=0, invalid=762 0179: dt=36.288000, rms=0.580 (0.176%), neg=0, invalid=762 0180: dt=145.152000, rms=0.579 (0.110%), neg=0, invalid=762 0181: dt=82.944000, rms=0.579 (0.126%), neg=0, invalid=762 0182: dt=62.208000, rms=0.578 (0.048%), neg=0, invalid=762 0183: dt=62.208000, rms=0.578 (0.080%), neg=0, invalid=762 0184: dt=62.208000, rms=0.577 (0.109%), neg=0, invalid=762 0185: dt=62.208000, rms=0.576 (0.144%), neg=0, invalid=762 0186: dt=62.208000, rms=0.576 (0.157%), neg=0, invalid=762 0187: dt=62.208000, rms=0.574 (0.212%), neg=0, invalid=762 0188: dt=62.208000, rms=0.573 (0.225%), neg=0, invalid=762 0189: dt=62.208000, rms=0.572 (0.214%), neg=0, invalid=762 0190: dt=62.208000, rms=0.571 (0.210%), neg=0, invalid=762 0191: dt=62.208000, rms=0.569 (0.225%), neg=0, invalid=762 0192: dt=62.208000, rms=0.568 (0.243%), neg=0, invalid=762 0193: dt=62.208000, rms=0.567 (0.230%), neg=0, invalid=762 0194: dt=62.208000, rms=0.565 (0.202%), neg=0, invalid=762 0195: dt=62.208000, rms=0.564 (0.185%), neg=0, invalid=762 0196: dt=62.208000, rms=0.563 (0.209%), neg=0, invalid=762 0197: dt=62.208000, rms=0.562 (0.193%), neg=0, invalid=762 0198: dt=62.208000, rms=0.561 (0.161%), neg=0, invalid=762 0199: dt=62.208000, rms=0.561 (0.019%), neg=0, invalid=762 0200: dt=62.208000, rms=0.561 (0.022%), neg=0, invalid=762 0201: dt=62.208000, rms=0.561 (0.052%), neg=0, invalid=762 0202: dt=62.208000, rms=0.560 (0.078%), neg=0, invalid=762 0203: dt=62.208000, rms=0.560 (0.069%), neg=0, invalid=762 0204: dt=62.208000, rms=0.560 (0.059%), neg=0, invalid=762 0205: dt=62.208000, rms=0.559 (0.075%), neg=0, invalid=762 0206: dt=62.208000, rms=0.559 (0.094%), neg=0, invalid=762 0207: dt=62.208000, rms=0.558 (0.097%), neg=0, invalid=762 0208: dt=15.552000, rms=0.558 (0.002%), neg=0, invalid=762 0209: dt=1.944000, rms=0.558 (0.002%), neg=0, invalid=762 0210: dt=0.972000, rms=0.558 (-0.000%), neg=0, invalid=762 0211: dt=1.620000, rms=0.558 (0.000%), neg=0, invalid=762 0212: dt=0.141750, rms=0.558 (0.001%), neg=0, invalid=762 0213: dt=0.035437, rms=0.558 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=762 0214: dt=73.580838, rms=0.557 (0.322%), neg=0, invalid=762 0215: dt=124.416000, rms=0.556 (0.182%), neg=0, invalid=762 0216: dt=36.288000, rms=0.556 (0.074%), neg=0, invalid=762 0217: dt=414.720000, rms=0.555 (0.187%), neg=0, invalid=762 0218: dt=36.288000, rms=0.554 (0.111%), neg=0, invalid=762 0219: dt=145.152000, rms=0.554 (0.079%), neg=0, invalid=762 0220: dt=62.208000, rms=0.553 (0.039%), neg=0, invalid=762 0221: dt=62.208000, rms=0.553 (0.024%), neg=0, invalid=762 0222: dt=62.208000, rms=0.553 (0.047%), neg=0, invalid=762 0223: dt=62.208000, rms=0.553 (0.081%), neg=0, invalid=762 0224: dt=62.208000, rms=0.552 (0.074%), neg=0, invalid=762 0225: dt=62.208000, rms=0.552 (0.080%), neg=0, invalid=762 0226: dt=62.208000, rms=0.551 (0.093%), neg=0, invalid=762 0227: dt=62.208000, rms=0.551 (0.108%), neg=0, invalid=762 0228: dt=62.208000, rms=0.550 (0.098%), neg=0, invalid=762 0229: dt=62.208000, rms=0.550 (0.094%), neg=0, invalid=762 0230: dt=62.208000, rms=0.549 (0.085%), neg=0, invalid=762 0231: dt=62.208000, rms=0.548 (0.112%), neg=0, invalid=762 0232: dt=62.208000, rms=0.548 (0.100%), neg=0, invalid=762 0233: dt=62.208000, rms=0.547 (0.095%), neg=0, invalid=762 0234: dt=62.208000, rms=0.547 (0.069%), neg=0, invalid=762 0235: dt=62.208000, rms=0.546 (0.108%), neg=0, invalid=762 0236: dt=62.208000, rms=0.546 (0.087%), neg=0, invalid=762 0237: dt=62.208000, rms=0.545 (0.093%), neg=0, invalid=762 0238: dt=62.208000, rms=0.545 (0.065%), neg=0, invalid=762 0239: dt=62.208000, rms=0.545 (0.088%), neg=0, invalid=762 0240: dt=62.208000, rms=0.544 (0.073%), neg=0, invalid=762 0241: dt=62.208000, rms=0.544 (0.078%), neg=0, invalid=762 0242: dt=62.208000, rms=0.543 (0.066%), neg=0, invalid=762 0243: dt=62.208000, rms=0.543 (0.076%), neg=0, invalid=762 0244: dt=62.208000, rms=0.543 (0.070%), neg=0, invalid=762 0245: dt=62.208000, rms=0.542 (0.066%), neg=0, invalid=762 0246: dt=62.208000, rms=0.542 (0.061%), neg=0, invalid=762 0247: dt=62.208000, rms=0.542 (0.072%), neg=0, invalid=762 0248: dt=62.208000, rms=0.541 (0.058%), neg=0, invalid=762 0249: dt=62.208000, rms=0.541 (-0.006%), neg=0, invalid=762 0250: dt=25.920000, rms=0.541 (0.002%), neg=0, invalid=762 0251: dt=124.416000, rms=0.541 (0.010%), neg=0, invalid=762 0252: dt=9.072000, rms=0.541 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.549, neg=0, invalid=762 0253: dt=44.800000, rms=0.545 (0.819%), neg=0, invalid=762 0254: dt=11.200000, rms=0.543 (0.338%), neg=0, invalid=762 0255: dt=0.600000, rms=0.543 (0.011%), neg=0, invalid=762 0256: dt=0.009375, rms=0.543 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=762 0257: dt=38.041298, rms=0.539 (0.757%), neg=0, invalid=762 0258: dt=29.310145, rms=0.537 (0.466%), neg=0, invalid=762 0259: dt=25.600000, rms=0.535 (0.368%), neg=0, invalid=762 0260: dt=32.000000, rms=0.533 (0.325%), neg=0, invalid=762 0261: dt=25.542169, rms=0.532 (0.302%), neg=0, invalid=762 0262: dt=25.600000, rms=0.530 (0.275%), neg=0, invalid=762 0263: dt=32.000000, rms=0.529 (0.236%), neg=0, invalid=762 0264: dt=24.671756, rms=0.527 (0.261%), neg=0, invalid=762 0265: dt=25.600000, rms=0.526 (0.204%), neg=0, invalid=762 0266: dt=32.000000, rms=0.525 (0.216%), neg=0, invalid=762 0267: dt=23.389558, rms=0.524 (0.179%), neg=0, invalid=762 0268: dt=32.000000, rms=0.523 (0.204%), neg=0, invalid=762 0269: dt=24.640000, rms=0.522 (0.158%), neg=0, invalid=762 0270: dt=25.600000, rms=0.522 (0.170%), neg=0, invalid=762 0271: dt=25.600000, rms=0.521 (0.121%), neg=0, invalid=762 0272: dt=25.600000, rms=0.520 (0.160%), neg=0, invalid=762 0273: dt=25.600000, rms=0.520 (0.105%), neg=0, invalid=762 0274: dt=32.000000, rms=0.519 (0.161%), neg=0, invalid=762 0275: dt=9.600000, rms=0.518 (0.073%), neg=0, invalid=762 0276: dt=0.175000, rms=0.518 (0.012%), neg=0, invalid=762 0277: dt=0.175000, rms=0.518 (0.001%), neg=0, invalid=762 0278: dt=0.087500, rms=0.518 (0.001%), neg=0, invalid=762 0279: dt=0.010937, rms=0.518 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.535, neg=0, invalid=762 0280: dt=2.880000, rms=0.534 (0.165%), neg=0, invalid=762 0281: dt=1.008000, rms=0.534 (0.006%), neg=0, invalid=762 0282: dt=1.008000, rms=0.534 (0.007%), neg=0, invalid=762 0283: dt=1.008000, rms=0.534 (0.001%), neg=0, invalid=762 0284: dt=1.008000, rms=0.534 (-0.034%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0285: dt=0.000000, rms=0.534 (0.127%), neg=0, invalid=762 0286: dt=0.000000, rms=0.534 (0.000%), neg=0, invalid=762 0287: dt=0.150000, rms=0.534 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0288: dt=1.024000, rms=0.562 (0.217%), neg=0, invalid=762 0289: dt=0.096000, rms=0.562 (-0.002%), neg=0, invalid=762 0290: dt=0.096000, rms=0.562 (0.001%), neg=0, invalid=762 0291: dt=0.096000, rms=0.562 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.562, neg=0, invalid=762 0292: dt=1.280000, rms=0.561 (0.213%), neg=0, invalid=762 0293: dt=0.112000, rms=0.561 (-0.001%), neg=0, invalid=762 0294: dt=0.112000, rms=0.561 (0.001%), neg=0, invalid=762 0295: dt=0.112000, rms=0.561 (-0.001%), 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=0.525, neg=0, invalid=762 0296: dt=0.448000, rms=0.511 (2.674%), neg=0, invalid=762 0297: dt=0.448000, rms=0.507 (0.704%), neg=0, invalid=762 0298: dt=0.448000, rms=0.505 (0.407%), neg=0, invalid=762 0299: dt=0.448000, rms=0.504 (0.261%), neg=0, invalid=762 0300: dt=0.448000, rms=0.503 (0.193%), neg=0, invalid=762 0301: dt=0.448000, rms=0.502 (0.148%), neg=0, invalid=762 0302: dt=0.448000, rms=0.501 (0.115%), neg=0, invalid=762 0303: dt=0.448000, rms=0.501 (0.095%), neg=0, invalid=762 0304: dt=0.448000, rms=0.500 (0.078%), neg=0, invalid=762 0305: dt=0.448000, rms=0.500 (0.059%), neg=0, invalid=762 0306: dt=0.448000, rms=0.500 (0.059%), neg=0, invalid=762 0307: dt=0.448000, rms=0.500 (0.040%), neg=0, invalid=762 0308: dt=0.448000, rms=0.499 (0.046%), neg=0, invalid=762 0309: dt=0.448000, rms=0.499 (0.069%), neg=0, invalid=762 0310: dt=0.448000, rms=0.499 (0.082%), neg=0, invalid=762 0311: dt=0.448000, rms=0.498 (0.091%), neg=0, invalid=762 0312: dt=0.448000, rms=0.498 (0.008%), neg=0, invalid=762 0313: dt=0.448000, rms=0.498 (0.009%), neg=0, invalid=762 0314: dt=0.448000, rms=0.498 (0.000%), neg=0, invalid=762 0315: dt=0.320000, rms=0.498 (0.009%), neg=0, invalid=762 0316: dt=0.384000, rms=0.498 (0.011%), neg=0, invalid=762 0317: dt=0.192000, rms=0.498 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=762 0318: dt=0.448000, rms=0.495 (0.812%), neg=0, invalid=762 0319: dt=0.448000, rms=0.494 (0.086%), neg=0, invalid=762 0320: dt=0.448000, rms=0.494 (0.026%), neg=0, invalid=762 0321: dt=0.448000, rms=0.494 (0.007%), neg=0, invalid=762 0322: dt=0.448000, rms=0.494 (0.001%), neg=0, invalid=762 0323: dt=0.224000, rms=0.494 (-0.005%), 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=0.492, neg=0, invalid=762 0324: dt=55.488000, rms=0.492 (0.170%), neg=0, invalid=762 0325: dt=0.000000, rms=0.492 (0.002%), neg=0, invalid=762 0326: dt=0.850000, rms=0.492 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=762 0327: dt=23.120000, rms=0.492 (0.146%), neg=0, invalid=762 0328: dt=18.496000, rms=0.492 (-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=0.492, neg=0, invalid=762 0329: dt=36.288000, rms=0.491 (0.260%), neg=0, invalid=762 0330: dt=103.680000, rms=0.490 (0.137%), neg=0, invalid=762 0331: dt=103.680000, rms=0.490 (0.111%), neg=0, invalid=762 0332: dt=103.680000, rms=0.489 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0333: dt=103.680000, rms=0.489 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0334: dt=36.288000, rms=0.488 (0.333%), neg=0, invalid=762 0335: dt=145.152000, rms=0.487 (0.284%), neg=0, invalid=762 0336: dt=36.288000, rms=0.486 (0.110%), neg=0, invalid=762 0337: dt=36.288000, rms=0.486 (0.059%), neg=0, invalid=762 0338: dt=36.288000, rms=0.486 (0.064%), neg=0, invalid=762 0339: dt=36.288000, rms=0.486 (0.069%), neg=0, invalid=762 0340: dt=36.288000, rms=0.485 (0.066%), neg=0, invalid=762 0341: dt=36.288000, rms=0.485 (0.095%), neg=0, invalid=762 0342: dt=36.288000, rms=0.484 (0.096%), neg=0, invalid=762 0343: dt=36.288000, rms=0.484 (0.096%), neg=0, invalid=762 0344: dt=25.920000, rms=0.484 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.485, neg=0, invalid=762 iter 0, gcam->neg = 9 after 0 iterations, nbhd size=0, neg = 0 0345: dt=32.000000, rms=0.481 (0.764%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0346: dt=44.800000, rms=0.478 (0.572%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0347: dt=11.200000, rms=0.477 (0.212%), neg=0, invalid=762 0348: dt=11.200000, rms=0.477 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0349: dt=11.200000, rms=0.476 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0350: dt=11.200000, rms=0.475 (0.212%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0351: dt=11.200000, rms=0.474 (0.273%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 6 iterations, nbhd size=0, neg = 0 0352: dt=11.200000, rms=0.473 (0.257%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 0353: dt=11.200000, rms=0.472 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0354: dt=11.200000, rms=0.471 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=0, neg = 0 0355: dt=11.200000, rms=0.470 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 12 iterations, nbhd size=1, neg = 0 0356: dt=11.200000, rms=0.469 (0.143%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0357: dt=11.200000, rms=0.469 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0358: dt=11.200000, rms=0.468 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=0, neg = 0 0359: dt=11.200000, rms=0.467 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0360: dt=11.200000, rms=0.467 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 0361: dt=11.200000, rms=0.466 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=0, neg = 0 0362: dt=11.200000, rms=0.466 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 0363: dt=11.200000, rms=0.465 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 0364: dt=44.800000, rms=0.465 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 16 iterations, nbhd size=1, neg = 0 0365: dt=44.800000, rms=0.465 (-0.090%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0366: dt=32.000000, rms=0.462 (0.633%), neg=0, invalid=762 0367: dt=32.000000, rms=0.461 (0.300%), neg=0, invalid=762 0368: dt=21.389474, rms=0.460 (0.150%), neg=0, invalid=762 0369: dt=21.389474, rms=0.460 (0.136%), neg=0, invalid=762 0370: dt=21.389474, rms=0.459 (0.148%), neg=0, invalid=762 0371: dt=21.389474, rms=0.458 (0.160%), neg=0, invalid=762 0372: dt=21.389474, rms=0.458 (0.102%), neg=0, invalid=762 0373: dt=21.389474, rms=0.457 (0.095%), neg=0, invalid=762 0374: dt=44.800000, rms=0.457 (0.086%), neg=0, invalid=762 0375: dt=44.800000, rms=0.457 (-0.081%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0376: dt=2.814815, rms=0.463 (0.172%), neg=0, invalid=762 0377: dt=1.008000, rms=0.463 (0.008%), neg=0, invalid=762 0378: dt=1.008000, rms=0.463 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0379: dt=4.032000, rms=0.463 (0.202%), neg=0, invalid=762 0380: dt=3.456000, rms=0.463 (0.016%), neg=0, invalid=762 0381: dt=3.456000, rms=0.463 (0.015%), neg=0, invalid=762 0382: dt=3.456000, rms=0.463 (-0.023%), 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 0383: dt=0.000000, rms=0.472 (0.159%), neg=0, invalid=762 0384: 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 0385: dt=0.448000, rms=0.472 (0.188%), neg=0, invalid=762 0386: dt=0.384000, rms=0.472 (0.010%), neg=0, invalid=762 0387: dt=0.384000, rms=0.472 (0.000%), neg=0, invalid=762 0388: dt=0.384000, rms=0.472 (-0.045%), 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=0.460, neg=0, invalid=762 iter 0, gcam->neg = 796 after 13 iterations, nbhd size=1, neg = 0 0389: dt=2.112594, rms=0.432 (6.237%), neg=0, invalid=762 0390: dt=0.028000, rms=0.432 (0.023%), neg=0, invalid=762 0391: dt=0.028000, rms=0.432 (0.001%), neg=0, invalid=762 0392: dt=0.028000, rms=0.432 (-0.031%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0393: dt=0.048000, rms=0.432 (0.233%), neg=0, invalid=762 0394: dt=0.006000, rms=0.432 (-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=0.418, neg=0, invalid=762 0395: dt=1.734000, rms=0.418 (0.000%), neg=0, invalid=762 0396: dt=0.003613, rms=0.418 (0.000%), neg=0, invalid=762 0397: dt=0.003613, rms=0.418 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0398: dt=32.368000, rms=0.418 (0.004%), neg=0, invalid=762 0399: dt=32.368000, rms=0.418 (0.002%), neg=0, invalid=762 0400: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=762 0401: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=762 0402: dt=32.368000, rms=0.418 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0403: dt=7.776000, rms=0.418 (0.008%), neg=0, invalid=762 0404: dt=0.324000, rms=0.418 (0.000%), neg=0, invalid=762 0405: dt=0.324000, rms=0.418 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0406: dt=103.680000, rms=0.418 (0.066%), neg=0, invalid=762 0407: dt=36.288000, rms=0.417 (0.047%), neg=0, invalid=762 0408: dt=36.288000, rms=0.417 (0.014%), neg=0, invalid=762 0409: dt=36.288000, rms=0.417 (0.024%), neg=0, invalid=762 0410: dt=36.288000, rms=0.417 (0.030%), neg=0, invalid=762 0411: dt=36.288000, rms=0.417 (0.032%), neg=0, invalid=762 0412: dt=36.288000, rms=0.417 (0.028%), neg=0, invalid=762 0413: dt=36.288000, rms=0.417 (0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 0414: dt=11.200000, rms=0.417 (0.096%), neg=0, invalid=762 0415: dt=9.600000, rms=0.417 (0.023%), neg=0, invalid=762 0416: dt=9.600000, rms=0.417 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0417: dt=9.600000, rms=0.417 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0418: dt=32.000000, rms=0.415 (0.398%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0419: dt=32.000000, rms=0.414 (0.268%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0420: dt=25.600000, rms=0.414 (0.098%), neg=0, invalid=762 0421: dt=25.600000, rms=0.413 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0422: dt=25.600000, rms=0.412 (0.172%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0423: dt=25.600000, rms=0.412 (0.210%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=1, neg = 0 0424: dt=25.600000, rms=0.411 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 11 iterations, nbhd size=1, neg = 0 0425: dt=25.600000, rms=0.410 (0.194%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 12 iterations, nbhd size=1, neg = 0 0426: dt=25.600000, rms=0.410 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 4 iterations, nbhd size=0, neg = 0 0427: dt=25.600000, rms=0.409 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 19 iterations, nbhd size=1, neg = 0 0428: dt=25.600000, rms=0.409 (0.057%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 9 iterations, nbhd size=0, neg = 0 0429: dt=25.600000, rms=0.408 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 11 iterations, nbhd size=1, neg = 0 0430: dt=25.600000, rms=0.408 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0431: dt=25.600000, rms=0.408 (0.024%), neg=0, invalid=762 0432: dt=25.600000, rms=0.408 (0.031%), neg=0, invalid=762 0433: dt=25.600000, rms=0.408 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0434: dt=25.600000, rms=0.408 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0435: dt=25.600000, rms=0.408 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0436: dt=2.304000, rms=0.412 (0.020%), neg=0, invalid=762 0437: dt=0.576000, rms=0.412 (0.001%), neg=0, invalid=762 0438: dt=0.576000, rms=0.412 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0439: dt=4.750000, rms=0.412 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0440: dt=4.032000, rms=0.412 (0.024%), neg=0, invalid=762 0441: dt=4.032000, rms=0.412 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0442: dt=4.032000, rms=0.412 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0443: dt=4.032000, rms=0.412 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0444: dt=0.000050, rms=0.419 (0.000%), neg=0, invalid=762 0445: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0446: dt=0.000000, rms=0.419 (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=0.407, neg=0, invalid=762 iter 0, gcam->neg = 685 after 18 iterations, nbhd size=1, neg = 0 0447: dt=1.168436, rms=0.397 (2.317%), neg=0, invalid=762 0448: dt=0.000023, rms=0.397 (0.000%), neg=0, invalid=762 0449: dt=0.000023, rms=0.397 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=762 0450: dt=0.064000, rms=0.397 (0.018%), neg=0, invalid=762 0451: dt=0.028000, rms=0.397 (0.003%), neg=0, invalid=762 0452: dt=0.028000, rms=0.397 (0.001%), neg=0, invalid=762 0453: dt=0.028000, rms=0.397 (-0.008%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 24 minutes and 25 seconds. mri_ca_register utimesec 9565.657798 mri_ca_register stimesec 9.174605 mri_ca_register ru_maxrss 1341756 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4156821 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62952 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4206 mri_ca_register ru_nivcsw 34739 FSRUNTIME@ mri_ca_register 2.4070 hours 2 threads #-------------------------------------- #@# SubCort Seg Sun Oct 8 04:31:49 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-604 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-6.0.0/0050566/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 2 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.36 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 = 0.09388 (12) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (730 voxels, overlap=0.233) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (730 voxels, peak = 13), gca=13.3 gca peak = 0.17677 (13) mri peak = 0.08343 (12) Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (868 voxels, overlap=0.842) Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (868 voxels, peak = 10), gca=10.1 gca peak = 0.28129 (95) mri peak = 0.09037 (90) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (751 voxels, overlap=1.018) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (751 voxels, peak = 89), gca=88.8 gca peak = 0.16930 (96) mri peak = 0.10694 (94) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (692 voxels, overlap=1.013) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (692 voxels, peak = 94), gca=93.6 gca peak = 0.24553 (55) mri peak = 0.08758 (60) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1056 voxels, overlap=1.007) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1056 voxels, peak = 57), gca=57.5 gca peak = 0.30264 (59) mri peak = 0.09937 (58) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (860 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (860 voxels, peak = 60), gca=60.5 gca peak = 0.07580 (103) mri peak = 0.09470 (102) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32978 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32978 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.10508 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (33541 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (33541 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04317 (55) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (39158 voxels, overlap=0.911) Left_Cerebral_Cortex (3): linear fit = 0.94 x + 0.0 (39158 voxels, peak = 55), gca=54.8 gca peak = 0.11620 (58) mri peak = 0.04299 (52) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (39473 voxels, overlap=0.918) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (39473 voxels, peak = 53), gca=53.1 gca peak = 0.30970 (66) mri peak = 0.12730 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, peak = 66), gca=66.0 gca peak = 0.15280 (69) mri peak = 0.15306 (67) Left_Caudate (11): linear fit = 0.89 x + 0.0 (1078 voxels, overlap=0.415) Left_Caudate (11): linear fit = 0.89 x + 0.0 (1078 voxels, peak = 62), gca=61.8 gca peak = 0.13902 (56) mri peak = 0.05693 (56) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (37288 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (37288 voxels, peak = 55), gca=55.2 gca peak = 0.14777 (55) mri peak = 0.05897 (56) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (37289 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (37289 voxels, peak = 57), gca=57.5 gca peak = 0.16765 (84) mri peak = 0.10502 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5911 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5911 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.08673 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7171 voxels, overlap=0.557) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7171 voxels, peak = 91), gca=91.1 gca peak = 0.29869 (57) mri peak = 0.09770 (58) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (530 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (530 voxels, peak = 55), gca=55.0 gca peak = 0.33601 (57) mri peak = 0.13066 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (575 voxels, overlap=0.983) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (575 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.09167 (82) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3720 voxels, overlap=0.915) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3720 voxels, peak = 86), gca=85.9 gca peak = 0.11793 (83) mri peak = 0.07687 (82) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, overlap=0.974) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, peak = 83), gca=83.0 gca peak = 0.08324 (81) mri peak = 0.08470 (75) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1889 voxels, overlap=0.795) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1889 voxels, peak = 77), gca=76.5 gca peak = 0.10360 (77) mri peak = 0.07397 (72) Right_Putamen (51): linear fit = 0.95 x + 0.0 (1778 voxels, overlap=0.750) Right_Putamen (51): linear fit = 0.95 x + 0.0 (1778 voxels, peak = 74), gca=73.5 gca peak = 0.08424 (78) mri peak = 0.07501 (85) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12972 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12972 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.07138 (97) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1668 voxels, overlap=0.756) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1668 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.06720 (97) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1757 voxels, overlap=0.725) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1757 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.07823 (33) gca peak = 0.19357 (14) mri peak = 0.10541 (12) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (349 voxels, overlap=0.713) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (349 voxels, peak = 10), gca=9.9 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 0.99 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.71 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19552 (12) mri peak = 0.09388 (12) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (730 voxels, overlap=0.922) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (730 voxels, peak = 12), gca=12.4 gca peak = 0.23646 (10) mri peak = 0.08343 (12) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (868 voxels, overlap=0.967) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (868 voxels, peak = 10), gca=10.4 gca peak = 0.27117 (88) mri peak = 0.09037 (90) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (751 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (751 voxels, peak = 87), gca=86.7 gca peak = 0.20112 (94) mri peak = 0.10694 (94) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (692 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (692 voxels, peak = 95), gca=95.4 gca peak = 0.28858 (58) mri peak = 0.08758 (60) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1056 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1056 voxels, peak = 59), gca=59.4 gca peak = 0.26523 (61) mri peak = 0.09937 (58) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (860 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (860 voxels, peak = 60), gca=60.1 gca peak = 0.07610 (105) mri peak = 0.09470 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32978 voxels, overlap=0.749) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32978 voxels, peak = 104), gca=104.5 gca peak = 0.07820 (106) mri peak = 0.10508 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33541 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (33541 voxels, peak = 106), gca=106.0 gca peak = 0.10323 (55) mri peak = 0.04317 (55) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (39158 voxels, overlap=0.998) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (39158 voxels, peak = 54), gca=54.2 gca peak = 0.12626 (53) mri peak = 0.04299 (52) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (39473 voxels, overlap=0.986) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (39473 voxels, peak = 55), gca=55.4 gca peak = 0.30217 (66) mri peak = 0.12730 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1031 voxels, peak = 66), gca=66.0 gca peak = 0.13943 (68) mri peak = 0.15306 (67) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1078 voxels, overlap=0.864) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1078 voxels, peak = 69), gca=69.0 gca peak = 0.14510 (55) mri peak = 0.05693 (56) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (37288 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (37288 voxels, peak = 55), gca=55.0 gca peak = 0.14202 (57) mri peak = 0.05897 (56) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (37289 voxels, overlap=0.996) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (37289 voxels, peak = 55), gca=55.0 gca peak = 0.15888 (90) mri peak = 0.10502 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5911 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5911 voxels, peak = 90), gca=89.6 gca peak = 0.14988 (91) mri peak = 0.08673 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7171 voxels, overlap=0.956) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7171 voxels, peak = 91), gca=90.5 gca peak = 0.27905 (56) mri peak = 0.09770 (58) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (530 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (530 voxels, peak = 59), gca=58.5 gca peak = 0.29016 (60) mri peak = 0.13066 (59) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (575 voxels, overlap=1.006) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (575 voxels, peak = 62), gca=61.5 gca peak = 0.11376 (86) mri peak = 0.09167 (82) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3720 voxels, overlap=0.954) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3720 voxels, peak = 85), gca=84.7 gca peak = 0.12266 (83) mri peak = 0.07687 (82) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, overlap=0.971) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3809 voxels, peak = 83), gca=83.0 gca peak = 0.09390 (78) mri peak = 0.08470 (75) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1889 voxels, overlap=0.918) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1889 voxels, peak = 78), gca=78.0 gca peak = 0.11277 (72) mri peak = 0.07397 (72) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1778 voxels, overlap=0.940) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1778 voxels, peak = 71), gca=70.9 gca peak = 0.07149 (90) mri peak = 0.07501 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12972 voxels, overlap=0.847) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12972 voxels, peak = 90), gca=90.0 gca peak = 0.11321 (96) mri peak = 0.07138 (97) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1668 voxels, overlap=0.910) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1668 voxels, peak = 95), gca=94.6 gca peak = 0.14451 (91) mri peak = 0.06720 (97) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1757 voxels, overlap=0.931) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1757 voxels, peak = 93), gca=93.3 gca peak = 0.20920 (18) mri peak = 0.07823 (33) gca peak = 0.26059 (10) mri peak = 0.10541 (12) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (349 voxels, overlap=0.887) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (349 voxels, peak = 10), gca=10.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15047 (33) gca peak Left_Thalamus = 1.00000 (93) gca peak Third_Ventricle = 0.20920 (18) gca peak CSF = 0.29800 (26) gca peak Left_Accumbens_area = 0.60061 (56) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.22003 (24) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82280 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65783 (23) gca peak WM_hypointensities = 0.07165 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70887 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 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 49824 voxels changed in iteration 0 of unlikely voxel relabeling 64 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 27992 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 339 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 63868 changed. image ll: -2.099, PF=0.500 pass 2: 17777 changed. image ll: -2.099, PF=0.500 pass 3: 6160 changed. pass 4: 2435 changed. 30391 voxels changed in iteration 0 of unlikely voxel relabeling 162 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5290 voxels changed in iteration 0 of unlikely voxel relabeling 20 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5254 voxels changed in iteration 0 of unlikely voxel relabeling 91 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5004 voxels changed in iteration 0 of unlikely voxel relabeling 39 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3110.188179 mri_ca_label stimesec 1.727737 mri_ca_label ru_maxrss 2108668 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 760315 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 62944 mri_ca_label ru_oublock 456 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 289 mri_ca_label ru_nivcsw 4617 auto-labeling took 51 minutes and 6 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/transforms/cc_up.lta 0050566 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-6.0.0/0050566/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/norm.mgz 30853 voxels in left wm, 62494 in right wm, xrange [119, 129] searching rotation angles z=[-8 6], y=[-9 5] searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 global minimum found at slice 125.0, rotations (-1.94, -1.17) final transformation (x=125.0, yr=-1.943, zr=-1.166): 0.99922 0.02036 -0.03390 3.90892; -0.02035 0.99979 0.00069 0.49977; 0.03391 0.00000 0.99943 21.82046; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 130 102 eigenvectors: -0.00055 -0.00577 0.99998; -0.14033 -0.99009 -0.00579; 0.99011 -0.14033 -0.00026; error in mid anterior detected - correcting... writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Sun Oct 8 05:23:48 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Oct 8 05:23:48 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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... 1718 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 61 (61), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 60 (60), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 57 seconds. #-------------------------------------------- #@# Mask BFS Sun Oct 8 05:26:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1516277 voxels in mask (pct= 9.04) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Oct 8 05:26:47 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.4 +- 5.4 [79.0 --> 125.0] GM (71.0) : 69.4 +- 9.5 [30.0 --> 95.0] setting bottom of white matter range to 79.0 setting top of gray matter range to 88.5 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... 3572 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6263 filled 2005 bright non-wm voxels segmented. 1648 diagonally connected voxels added... white matter segmentation took 1.5 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... 61 voxels added to wm to prevent paths from MTL structures to cortex 3322 additional wm voxels added 0 additional wm voxels added SEG EDIT: 41562 voxels turned on, 42119 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 107 new 107 115,126,128 old 107 new 107 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 17 found - 17 modified | TOTAL: 39 pass 2 (xy-): 0 found - 17 modified | TOTAL: 39 pass 1 (yz+): 24 found - 24 modified | TOTAL: 63 pass 2 (yz+): 0 found - 24 modified | TOTAL: 63 pass 1 (yz-): 28 found - 28 modified | TOTAL: 91 pass 2 (yz-): 0 found - 28 modified | TOTAL: 91 pass 1 (xz+): 20 found - 20 modified | TOTAL: 111 pass 2 (xz+): 0 found - 20 modified | TOTAL: 111 pass 1 (xz-): 19 found - 19 modified | TOTAL: 130 pass 2 (xz-): 0 found - 19 modified | TOTAL: 130 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 10 found - 10 modified | TOTAL: 22 pass 2 (+++): 0 found - 10 modified | TOTAL: 22 pass 1 (+++): 10 found - 10 modified | TOTAL: 32 pass 2 (+++): 0 found - 10 modified | TOTAL: 32 pass 1 (+++): 12 found - 12 modified | TOTAL: 44 pass 2 (+++): 0 found - 12 modified | TOTAL: 44 Iteration Number : 1 pass 1 (++): 40 found - 40 modified | TOTAL: 40 pass 2 (++): 0 found - 40 modified | TOTAL: 40 pass 1 (+-): 47 found - 47 modified | TOTAL: 87 pass 2 (+-): 0 found - 47 modified | TOTAL: 87 pass 1 (--): 119 found - 119 modified | TOTAL: 206 pass 2 (--): 1 found - 120 modified | TOTAL: 207 pass 3 (--): 0 found - 120 modified | TOTAL: 207 pass 1 (-+): 35 found - 35 modified | TOTAL: 242 pass 2 (-+): 0 found - 35 modified | TOTAL: 242 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 5 found - 5 modified | TOTAL: 8 pass 2 (xy-): 0 found - 5 modified | TOTAL: 8 pass 1 (yz+): 4 found - 4 modified | TOTAL: 12 pass 2 (yz+): 0 found - 4 modified | TOTAL: 12 pass 1 (yz-): 3 found - 3 modified | TOTAL: 15 pass 2 (yz-): 0 found - 3 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 3 found - 3 modified | TOTAL: 20 pass 2 (xz-): 0 found - 3 modified | TOTAL: 20 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 1 found - 1 modified | TOTAL: 6 pass 2 (+-): 0 found - 1 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 2 found - 2 modified | TOTAL: 9 pass 2 (-+): 0 found - 2 modified | TOTAL: 9 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 (+-): 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 Iteration Number : 6 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 : 6 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 : 6 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 = 455 (out of 497909: 0.091382) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Oct 8 05:28:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 1.08085 -0.05724 -0.05528 4.52116; 0.06755 1.05155 0.32229 -78.07095; 0.03166 -0.33587 0.99870 44.39107; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.08085 -0.05724 -0.05528 4.52116; 0.06755 1.05155 0.32229 -78.07095; 0.03166 -0.33587 0.99870 44.39107; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1050 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (125, 119, 150), TAL = (3.0, 22.0, 9.0) talairach voxel to voxel transform 0.92051 0.06018 0.03153 -0.86359; -0.04550 0.85914 -0.27977 79.69904; -0.04448 0.28702 0.90621 -17.61836; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 119, 150) --> (3.0, 22.0, 9.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (3.00, 22.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 22.00, 9.00) SRC: (109.52, 135.10, 147.71) search lh wm seed point around talairach space (-15.00, 22.00, 9.00), SRC: (142.66, 133.46, 146.11) 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 Sun Oct 8 05:29:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 11 (out of 239637: 0.004590) 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: 1220 vertices, 1353 faces slice 50: 8286 vertices, 8599 faces slice 60: 18647 vertices, 19038 faces slice 70: 29951 vertices, 30363 faces slice 80: 40657 vertices, 41106 faces slice 90: 51941 vertices, 52388 faces slice 100: 62768 vertices, 63222 faces slice 110: 73733 vertices, 74203 faces slice 120: 84508 vertices, 85000 faces slice 130: 94892 vertices, 95374 faces slice 140: 105348 vertices, 105790 faces slice 150: 114063 vertices, 114500 faces slice 160: 122418 vertices, 122772 faces slice 170: 128274 vertices, 128570 faces slice 180: 132559 vertices, 132819 faces slice 190: 134822 vertices, 134980 faces slice 200: 134906 vertices, 135040 faces slice 210: 134906 vertices, 135040 faces slice 220: 134906 vertices, 135040 faces slice 230: 134906 vertices, 135040 faces slice 240: 134906 vertices, 135040 faces slice 250: 134906 vertices, 135040 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... 134906 voxel in cpt #1: X=-134 [v=134906,e=405120,f=270080] located at (-23.177553, -23.320089, -9.925511) For the whole surface: X=-134 [v=134906,e=405120,f=270080] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Oct 8 05:29:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 235310: 0.001700) 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: 937 vertices, 1014 faces slice 50: 6953 vertices, 7209 faces slice 60: 16590 vertices, 16985 faces slice 70: 27248 vertices, 27605 faces slice 80: 38276 vertices, 38665 faces slice 90: 48896 vertices, 49256 faces slice 100: 59629 vertices, 60033 faces slice 110: 69679 vertices, 70079 faces slice 120: 79888 vertices, 80273 faces slice 130: 90128 vertices, 90514 faces slice 140: 99718 vertices, 100102 faces slice 150: 108656 vertices, 109010 faces slice 160: 116359 vertices, 116663 faces slice 170: 121863 vertices, 122104 faces slice 180: 126187 vertices, 126394 faces slice 190: 128431 vertices, 128542 faces slice 200: 128566 vertices, 128644 faces slice 210: 128566 vertices, 128644 faces slice 220: 128566 vertices, 128644 faces slice 230: 128566 vertices, 128644 faces slice 240: 128566 vertices, 128644 faces slice 250: 128566 vertices, 128644 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... 128566 voxel in cpt #1: X=-78 [v=128566,e=385932,f=257288] located at (28.957212, -22.628572, -10.298430) For the whole surface: X=-78 [v=128566,e=385932,f=257288] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Oct 8 05:29:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun Oct 8 05:29:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 8532 of (8532 8535) to complete... Waiting for PID 8535 of (8532 8535) 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 (8532 8535) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun Oct 8 05:29:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun Oct 8 05:29:42 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 8580 of (8580 8583) to complete... Waiting for PID 8583 of (8580 8583) 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 = 46.8 mm, total surface area = 73098 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.087 (target=0.015) step 020: RMS=0.079 (target=0.015) step 025: RMS=0.073 (target=0.015) step 030: RMS=0.068 (target=0.015) step 035: RMS=0.064 (target=0.015) step 040: RMS=0.062 (target=0.015) step 045: RMS=0.059 (target=0.015) step 050: RMS=0.057 (target=0.015) step 055: RMS=0.056 (target=0.015) step 060: RMS=0.055 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 42.536533 mris_inflate stimesec 0.106983 mris_inflate ru_maxrss 196900 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28721 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9496 mris_inflate ru_oublock 9512 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2120 mris_inflate ru_nivcsw 3586 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.9 mm, total surface area = 69349 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.049 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 40.779800 mris_inflate stimesec 0.098984 mris_inflate ru_maxrss 187956 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26995 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9048 mris_inflate ru_oublock 9064 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2018 mris_inflate ru_nivcsw 3325 PIDs (8580 8583) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun Oct 8 05:30:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun Oct 8 05:30:25 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 8668 of (8668 8672) to complete... Waiting for PID 8672 of (8668 8672) 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 0.99 +- 0.62 (0.00-->6.31) (max @ vno 68929 --> 69966) face area 0.03 +- 0.04 (-0.25-->0.63) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.513, avgs=0 005/300: dt: 0.9000, rms radial error=175.255, avgs=0 010/300: dt: 0.9000, rms radial error=174.700, avgs=0 015/300: dt: 0.9000, rms radial error=173.970, avgs=0 020/300: dt: 0.9000, rms radial error=173.138, avgs=0 025/300: dt: 0.9000, rms radial error=172.249, avgs=0 030/300: dt: 0.9000, rms radial error=171.335, avgs=0 035/300: dt: 0.9000, rms radial error=170.405, avgs=0 040/300: dt: 0.9000, rms radial error=169.467, avgs=0 045/300: dt: 0.9000, rms radial error=168.527, avgs=0 050/300: dt: 0.9000, rms radial error=167.588, avgs=0 055/300: dt: 0.9000, rms radial error=166.653, avgs=0 060/300: dt: 0.9000, rms radial error=165.721, avgs=0 065/300: dt: 0.9000, rms radial error=164.793, avgs=0 070/300: dt: 0.9000, rms radial error=163.869, avgs=0 075/300: dt: 0.9000, rms radial error=162.950, avgs=0 080/300: dt: 0.9000, rms radial error=162.036, avgs=0 085/300: dt: 0.9000, rms radial error=161.127, avgs=0 090/300: dt: 0.9000, rms radial error=160.223, avgs=0 095/300: dt: 0.9000, rms radial error=159.324, avgs=0 100/300: dt: 0.9000, rms radial error=158.429, avgs=0 105/300: dt: 0.9000, rms radial error=157.541, avgs=0 110/300: dt: 0.9000, rms radial error=156.657, avgs=0 115/300: dt: 0.9000, rms radial error=155.777, avgs=0 120/300: dt: 0.9000, rms radial error=154.903, avgs=0 125/300: dt: 0.9000, rms radial error=154.033, avgs=0 130/300: dt: 0.9000, rms radial error=153.167, avgs=0 135/300: dt: 0.9000, rms radial error=152.306, avgs=0 140/300: dt: 0.9000, rms radial error=151.450, avgs=0 145/300: dt: 0.9000, rms radial error=150.598, avgs=0 150/300: dt: 0.9000, rms radial error=149.751, avgs=0 155/300: dt: 0.9000, rms radial error=148.909, avgs=0 160/300: dt: 0.9000, rms radial error=148.070, avgs=0 165/300: dt: 0.9000, rms radial error=147.237, avgs=0 170/300: dt: 0.9000, rms radial error=146.408, avgs=0 175/300: dt: 0.9000, rms radial error=145.583, avgs=0 180/300: dt: 0.9000, rms radial error=144.763, avgs=0 185/300: dt: 0.9000, rms radial error=143.948, avgs=0 190/300: dt: 0.9000, rms radial error=143.137, avgs=0 195/300: dt: 0.9000, rms radial error=142.331, avgs=0 200/300: dt: 0.9000, rms radial error=141.530, avgs=0 205/300: dt: 0.9000, rms radial error=140.732, avgs=0 210/300: dt: 0.9000, rms radial error=139.939, avgs=0 215/300: dt: 0.9000, rms radial error=139.151, avgs=0 220/300: dt: 0.9000, rms radial error=138.367, avgs=0 225/300: dt: 0.9000, rms radial error=137.587, avgs=0 230/300: dt: 0.9000, rms radial error=136.811, avgs=0 235/300: dt: 0.9000, rms radial error=136.040, avgs=0 240/300: dt: 0.9000, rms radial error=135.273, avgs=0 245/300: dt: 0.9000, rms radial error=134.511, avgs=0 250/300: dt: 0.9000, rms radial error=133.752, avgs=0 255/300: dt: 0.9000, rms radial error=132.999, avgs=0 260/300: dt: 0.9000, rms radial error=132.249, avgs=0 265/300: dt: 0.9000, rms radial error=131.503, avgs=0 270/300: dt: 0.9000, rms radial error=130.762, avgs=0 275/300: dt: 0.9000, rms radial error=130.025, avgs=0 280/300: dt: 0.9000, rms radial error=129.292, avgs=0 285/300: dt: 0.9000, rms radial error=128.562, avgs=0 290/300: dt: 0.9000, rms radial error=127.837, avgs=0 295/300: dt: 0.9000, rms radial error=127.116, avgs=0 300/300: dt: 0.9000, rms radial error=126.400, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15616.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 2 (K=40.0), pass 1, starting sse = 2671.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 3 (K=160.0), pass 1, starting sse = 340.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00197 epoch 4 (K=640.0), pass 1, starting sse = 52.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00749 final distance error %29.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 246.873469 mris_sphere stimesec 0.156976 mris_sphere ru_maxrss 197100 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 28770 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9536 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8376 mris_sphere ru_nivcsw 20486 FSRUNTIME@ mris_sphere 0.0682 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 1.01 +- 0.61 (0.00-->6.12) (max @ vno 59460 --> 60595) face area 0.03 +- 0.04 (-0.05-->0.63) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.323... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.046, avgs=0 005/300: dt: 0.9000, rms radial error=175.789, avgs=0 010/300: dt: 0.9000, rms radial error=175.237, avgs=0 015/300: dt: 0.9000, rms radial error=174.513, avgs=0 020/300: dt: 0.9000, rms radial error=173.689, avgs=0 025/300: dt: 0.9000, rms radial error=172.808, avgs=0 030/300: dt: 0.9000, rms radial error=171.895, avgs=0 035/300: dt: 0.9000, rms radial error=170.965, avgs=0 040/300: dt: 0.9000, rms radial error=170.028, avgs=0 045/300: dt: 0.9000, rms radial error=169.087, avgs=0 050/300: dt: 0.9000, rms radial error=168.148, avgs=0 055/300: dt: 0.9000, rms radial error=167.210, avgs=0 060/300: dt: 0.9000, rms radial error=166.276, avgs=0 065/300: dt: 0.9000, rms radial error=165.346, avgs=0 070/300: dt: 0.9000, rms radial error=164.422, avgs=0 075/300: dt: 0.9000, rms radial error=163.503, avgs=0 080/300: dt: 0.9000, rms radial error=162.588, avgs=0 085/300: dt: 0.9000, rms radial error=161.679, avgs=0 090/300: dt: 0.9000, rms radial error=160.774, avgs=0 095/300: dt: 0.9000, rms radial error=159.873, avgs=0 100/300: dt: 0.9000, rms radial error=158.978, avgs=0 105/300: dt: 0.9000, rms radial error=158.087, avgs=0 110/300: dt: 0.9000, rms radial error=157.200, avgs=0 115/300: dt: 0.9000, rms radial error=156.319, avgs=0 120/300: dt: 0.9000, rms radial error=155.442, avgs=0 125/300: dt: 0.9000, rms radial error=154.569, avgs=0 130/300: dt: 0.9000, rms radial error=153.701, avgs=0 135/300: dt: 0.9000, rms radial error=152.837, avgs=0 140/300: dt: 0.9000, rms radial error=151.979, avgs=0 145/300: dt: 0.9000, rms radial error=151.124, avgs=0 150/300: dt: 0.9000, rms radial error=150.275, avgs=0 155/300: dt: 0.9000, rms radial error=149.430, avgs=0 160/300: dt: 0.9000, rms radial error=148.590, avgs=0 165/300: dt: 0.9000, rms radial error=147.754, avgs=0 170/300: dt: 0.9000, rms radial error=146.923, avgs=0 175/300: dt: 0.9000, rms radial error=146.097, avgs=0 180/300: dt: 0.9000, rms radial error=145.275, avgs=0 185/300: dt: 0.9000, rms radial error=144.457, avgs=0 190/300: dt: 0.9000, rms radial error=143.644, avgs=0 195/300: dt: 0.9000, rms radial error=142.835, avgs=0 200/300: dt: 0.9000, rms radial error=142.031, avgs=0 205/300: dt: 0.9000, rms radial error=141.231, avgs=0 210/300: dt: 0.9000, rms radial error=140.436, avgs=0 215/300: dt: 0.9000, rms radial error=139.646, avgs=0 220/300: dt: 0.9000, rms radial error=138.859, avgs=0 225/300: dt: 0.9000, rms radial error=138.077, avgs=0 230/300: dt: 0.9000, rms radial error=137.300, avgs=0 235/300: dt: 0.9000, rms radial error=136.526, avgs=0 240/300: dt: 0.9000, rms radial error=135.757, avgs=0 245/300: dt: 0.9000, rms radial error=134.992, avgs=0 250/300: dt: 0.9000, rms radial error=134.231, avgs=0 255/300: dt: 0.9000, rms radial error=133.475, avgs=0 260/300: dt: 0.9000, rms radial error=132.723, avgs=0 265/300: dt: 0.9000, rms radial error=131.975, avgs=0 270/300: dt: 0.9000, rms radial error=131.231, avgs=0 275/300: dt: 0.9000, rms radial error=130.491, avgs=0 280/300: dt: 0.9000, rms radial error=129.755, avgs=0 285/300: dt: 0.9000, rms radial error=129.024, avgs=0 290/300: dt: 0.9000, rms radial error=128.296, avgs=0 295/300: dt: 0.9000, rms radial error=127.573, avgs=0 300/300: dt: 0.9000, rms radial error=126.854, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14809.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 2 (K=40.0), pass 1, starting sse = 2431.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 3 (K=160.0), pass 1, starting sse = 255.76 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/11 = 0.00890 epoch 4 (K=640.0), pass 1, starting sse = 19.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/13 = 0.00831 final distance error %26.45 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 242.156186 mris_sphere stimesec 0.176973 mris_sphere ru_maxrss 188160 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 27556 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9088 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8208 mris_sphere ru_nivcsw 18103 FSRUNTIME@ mris_sphere 0.0673 hours 1 threads PIDs (8668 8672) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sun Oct 8 05:34:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Oct 8 05:34:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Oct 8 05:34:31 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 lh #@# Fix Topology rh Sun Oct 8 05:34:31 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 rh Waiting for PID 8933 of (8933 8936) to complete... Waiting for PID 8936 of (8933 8936) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 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=-134 (nv=134906, nf=270080, ne=405120, g=68) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 28813 ambiguous faces found in tessellation segmenting defects... 50 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 15 into 12 -merging segment 43 into 37 48 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2964 (-4.6482) -vertex loglikelihood: -6.2890 (-3.1445) -normal dot loglikelihood: -3.6136 (-3.6136) -quad curv loglikelihood: -5.7849 (-2.8924) Total Loglikelihood : -24.9838 CORRECTING DEFECT 0 (vertices=94, convex hull=140, v0=67) After retessellation of defect 0 (v0=67), euler #=-40 (119149,354567,235378) : difference with theory (-45) = -5 CORRECTING DEFECT 1 (vertices=74, convex hull=122, v0=866) After retessellation of defect 1 (v0=866), euler #=-39 (119183,354720,235498) : difference with theory (-44) = -5 CORRECTING DEFECT 2 (vertices=306, convex hull=232, v0=2209) After retessellation of defect 2 (v0=2209), euler #=-38 (119300,355178,235840) : difference with theory (-43) = -5 CORRECTING DEFECT 3 (vertices=30, convex hull=72, v0=6846) After retessellation of defect 3 (v0=6846), euler #=-37 (119319,355264,235908) : difference with theory (-42) = -5 CORRECTING DEFECT 4 (vertices=88, convex hull=132, v0=7068) After retessellation of defect 4 (v0=7068), euler #=-36 (119338,355387,236013) : difference with theory (-41) = -5 CORRECTING DEFECT 5 (vertices=109, convex hull=109, v0=9079) After retessellation of defect 5 (v0=9079), euler #=-35 (119397,355614,236182) : difference with theory (-40) = -5 CORRECTING DEFECT 6 (vertices=311, convex hull=188, v0=9184) After retessellation of defect 6 (v0=9184), euler #=-34 (119448,355856,236374) : difference with theory (-39) = -5 CORRECTING DEFECT 7 (vertices=20, convex hull=28, v0=11170) After retessellation of defect 7 (v0=11170), euler #=-33 (119449,355867,236385) : difference with theory (-38) = -5 CORRECTING DEFECT 8 (vertices=417, convex hull=178, v0=11623) After retessellation of defect 8 (v0=11623), euler #=-32 (119640,356529,236857) : difference with theory (-37) = -5 CORRECTING DEFECT 9 (vertices=21, convex hull=67, v0=12130) After retessellation of defect 9 (v0=12130), euler #=-31 (119653,356589,236905) : difference with theory (-36) = -5 CORRECTING DEFECT 10 (vertices=8955, convex hull=1082, v0=13015) XL defect detected... After retessellation of defect 10 (v0=13015), euler #=-34 (119817,357670,237819) : difference with theory (-35) = -1 CORRECTING DEFECT 11 (vertices=148, convex hull=137, v0=16381) After retessellation of defect 11 (v0=16381), euler #=-33 (119877,357914,238004) : difference with theory (-34) = -1 CORRECTING DEFECT 12 (vertices=648, convex hull=277, v0=18307) After retessellation of defect 12 (v0=18307), euler #=-33 (120036,358547,238478) : difference with theory (-33) = 0 CORRECTING DEFECT 13 (vertices=98, convex hull=83, v0=27097) After retessellation of defect 13 (v0=27097), euler #=-32 (120080,358716,238604) : difference with theory (-32) = 0 CORRECTING DEFECT 14 (vertices=132, convex hull=125, v0=27604) normal vector of length zero at vertex 130549 with 3 faces normal vector of length zero at vertex 130549 with 3 faces After retessellation of defect 14 (v0=27604), euler #=-31 (120128,358916,238757) : difference with theory (-31) = 0 CORRECTING DEFECT 15 (vertices=249, convex hull=169, v0=35914) After retessellation of defect 15 (v0=35914), euler #=-30 (120230,359308,239048) : difference with theory (-30) = 0 CORRECTING DEFECT 16 (vertices=281, convex hull=229, v0=38363) After retessellation of defect 16 (v0=38363), euler #=-29 (120347,359777,239401) : difference with theory (-29) = 0 CORRECTING DEFECT 17 (vertices=94, convex hull=90, v0=45202) After retessellation of defect 17 (v0=45202), euler #=-28 (120380,359920,239512) : difference with theory (-28) = 0 CORRECTING DEFECT 18 (vertices=61, convex hull=73, v0=51598) After retessellation of defect 18 (v0=51598), euler #=-27 (120414,360053,239612) : difference with theory (-27) = 0 CORRECTING DEFECT 19 (vertices=28, convex hull=62, v0=51913) After retessellation of defect 19 (v0=51913), euler #=-26 (120423,360104,239655) : difference with theory (-26) = 0 CORRECTING DEFECT 20 (vertices=51, convex hull=97, v0=52373) After retessellation of defect 20 (v0=52373), euler #=-25 (120458,360250,239767) : difference with theory (-25) = 0 CORRECTING DEFECT 21 (vertices=47, convex hull=83, v0=53985) After retessellation of defect 21 (v0=53985), euler #=-24 (120490,360380,239866) : difference with theory (-24) = 0 CORRECTING DEFECT 22 (vertices=141, convex hull=168, v0=54971) normal vector of length zero at vertex 131494 with 4 faces normal vector of length zero at vertex 131496 with 4 faces normal vector of length zero at vertex 131496 with 4 faces normal vector of length zero at vertex 131496 with 4 faces normal vector of length zero at vertex 131508 with 4 faces normal vector of length zero at vertex 131508 with 4 faces normal vector of length zero at vertex 131508 with 4 faces After retessellation of defect 22 (v0=54971), euler #=-23 (120532,360582,240027) : difference with theory (-23) = 0 CORRECTING DEFECT 23 (vertices=37, convex hull=66, v0=56223) After retessellation of defect 23 (v0=56223), euler #=-22 (120550,360664,240092) : difference with theory (-22) = 0 CORRECTING DEFECT 24 (vertices=5, convex hull=26, v0=57303) After retessellation of defect 24 (v0=57303), euler #=-21 (120551,360675,240103) : difference with theory (-21) = 0 CORRECTING DEFECT 25 (vertices=25, convex hull=22, v0=59406) After retessellation of defect 25 (v0=59406), euler #=-20 (120555,360692,240117) : difference with theory (-20) = 0 CORRECTING DEFECT 26 (vertices=16, convex hull=46, v0=69489) After retessellation of defect 26 (v0=69489), euler #=-19 (120562,360731,240150) : difference with theory (-19) = 0 CORRECTING DEFECT 27 (vertices=8, convex hull=32, v0=69601) After retessellation of defect 27 (v0=69601), euler #=-18 (120563,360743,240162) : difference with theory (-18) = 0 CORRECTING DEFECT 28 (vertices=56, convex hull=112, v0=71664) After retessellation of defect 28 (v0=71664), euler #=-17 (120599,360894,240278) : difference with theory (-17) = 0 CORRECTING DEFECT 29 (vertices=9, convex hull=13, v0=76603) After retessellation of defect 29 (v0=76603), euler #=-16 (120600,360899,240283) : difference with theory (-16) = 0 CORRECTING DEFECT 30 (vertices=96, convex hull=101, v0=79241) After retessellation of defect 30 (v0=79241), euler #=-15 (120639,361062,240408) : difference with theory (-15) = 0 CORRECTING DEFECT 31 (vertices=125, convex hull=94, v0=82520) After retessellation of defect 31 (v0=82520), euler #=-14 (120690,361255,240551) : difference with theory (-14) = 0 CORRECTING DEFECT 32 (vertices=132, convex hull=100, v0=91064) After retessellation of defect 32 (v0=91064), euler #=-13 (120736,361437,240688) : difference with theory (-13) = 0 CORRECTING DEFECT 33 (vertices=185, convex hull=173, v0=91704) After retessellation of defect 33 (v0=91704), euler #=-12 (120819,361766,240935) : difference with theory (-12) = 0 CORRECTING DEFECT 34 (vertices=44, convex hull=77, v0=92508) After retessellation of defect 34 (v0=92508), euler #=-11 (120846,361879,241022) : difference with theory (-11) = 0 CORRECTING DEFECT 35 (vertices=9, convex hull=15, v0=96794) After retessellation of defect 35 (v0=96794), euler #=-10 (120848,361890,241032) : difference with theory (-10) = 0 CORRECTING DEFECT 36 (vertices=1537, convex hull=472, v0=100004) XL defect detected... After retessellation of defect 36 (v0=100004), euler #=-9 (121000,362606,241597) : difference with theory (-9) = 0 CORRECTING DEFECT 37 (vertices=26, convex hull=30, v0=100182) After retessellation of defect 37 (v0=100182), euler #=-8 (121009,362643,241626) : difference with theory (-8) = 0 CORRECTING DEFECT 38 (vertices=67, convex hull=53, v0=102087) After retessellation of defect 38 (v0=102087), euler #=-7 (121024,362710,241679) : difference with theory (-7) = 0 CORRECTING DEFECT 39 (vertices=242, convex hull=93, v0=106163) After retessellation of defect 39 (v0=106163), euler #=-6 (121037,362796,241753) : difference with theory (-6) = 0 CORRECTING DEFECT 40 (vertices=154, convex hull=116, v0=107841) After retessellation of defect 40 (v0=107841), euler #=-5 (121068,362939,241866) : difference with theory (-5) = 0 CORRECTING DEFECT 41 (vertices=221, convex hull=86, v0=110725) After retessellation of defect 41 (v0=110725), euler #=-4 (121118,363132,242010) : difference with theory (-4) = 0 CORRECTING DEFECT 42 (vertices=108, convex hull=113, v0=123801) After retessellation of defect 42 (v0=123801), euler #=-3 (121169,363341,242169) : difference with theory (-3) = 0 CORRECTING DEFECT 43 (vertices=89, convex hull=91, v0=124505) After retessellation of defect 43 (v0=124505), euler #=-2 (121206,363492,242284) : difference with theory (-2) = 0 CORRECTING DEFECT 44 (vertices=10, convex hull=29, v0=126929) After retessellation of defect 44 (v0=126929), euler #=-1 (121207,363505,242297) : difference with theory (-1) = 0 CORRECTING DEFECT 45 (vertices=48, convex hull=72, v0=127314) After retessellation of defect 45 (v0=127314), euler #=0 (121224,363587,242363) : difference with theory (0) = 0 CORRECTING DEFECT 46 (vertices=76, convex hull=97, v0=127734) After retessellation of defect 46 (v0=127734), euler #=1 (121272,363772,242501) : difference with theory (1) = 0 CORRECTING DEFECT 47 (vertices=57, convex hull=75, v0=128038) After retessellation of defect 47 (v0=128038), euler #=2 (121292,363870,242580) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.30 (0.03-->20.04) (max @ vno 82463 --> 87703) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.30 (0.03-->20.04) (max @ vno 82463 --> 87703) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 115 mutations (30.2%), 266 crossovers (69.8%), 2536 vertices were eliminated building final representation... 13614 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=121292, nf=242580, ne=363870, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 216.7 minutes 0 defective edges removing intersecting faces 000: 854 intersecting 001: 21 intersecting 002: 4 intersecting mris_fix_topology utimesec 13008.547400 mris_fix_topology stimesec 2.420632 mris_fix_topology ru_maxrss 676892 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 116465 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 2528 mris_fix_topology ru_oublock 11992 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 327 mris_fix_topology ru_nivcsw 24162 FSRUNTIME@ mris_fix_topology lh 3.6122 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050566 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=-78 (nv=128566, nf=257288, ne=385932, g=40) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 6950 ambiguous faces found in tessellation segmenting defects... 48 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 48 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4102 (-4.7051) -vertex loglikelihood: -6.2925 (-3.1462) -normal dot loglikelihood: -3.5568 (-3.5568) -quad curv loglikelihood: -6.1537 (-3.0769) Total Loglikelihood : -25.4131 CORRECTING DEFECT 0 (vertices=37, convex hull=47, v0=211) After retessellation of defect 0 (v0=211), euler #=-45 (124381,371574,247148) : difference with theory (-45) = 0 CORRECTING DEFECT 1 (vertices=6, convex hull=25, v0=3233) After retessellation of defect 1 (v0=3233), euler #=-44 (124382,371583,247157) : difference with theory (-44) = 0 CORRECTING DEFECT 2 (vertices=87, convex hull=111, v0=3442) After retessellation of defect 2 (v0=3442), euler #=-43 (124432,371779,247304) : difference with theory (-43) = 0 CORRECTING DEFECT 3 (vertices=42, convex hull=40, v0=4047) After retessellation of defect 3 (v0=4047), euler #=-42 (124439,371819,247338) : difference with theory (-42) = 0 CORRECTING DEFECT 4 (vertices=25, convex hull=71, v0=4547) After retessellation of defect 4 (v0=4547), euler #=-41 (124452,371887,247394) : difference with theory (-41) = 0 CORRECTING DEFECT 5 (vertices=76, convex hull=130, v0=7313) After retessellation of defect 5 (v0=7313), euler #=-40 (124494,372072,247538) : difference with theory (-40) = 0 CORRECTING DEFECT 6 (vertices=63, convex hull=128, v0=9734) After retessellation of defect 6 (v0=9734), euler #=-39 (124532,372240,247669) : difference with theory (-39) = 0 CORRECTING DEFECT 7 (vertices=229, convex hull=95, v0=10203) After retessellation of defect 7 (v0=10203), euler #=-38 (124576,372418,247804) : difference with theory (-38) = 0 CORRECTING DEFECT 8 (vertices=74, convex hull=84, v0=12513) After retessellation of defect 8 (v0=12513), euler #=-37 (124600,372526,247889) : difference with theory (-37) = 0 CORRECTING DEFECT 9 (vertices=19, convex hull=45, v0=13344) After retessellation of defect 9 (v0=13344), euler #=-36 (124611,372574,247927) : difference with theory (-36) = 0 CORRECTING DEFECT 10 (vertices=90, convex hull=100, v0=18771) After retessellation of defect 10 (v0=18771), euler #=-35 (124653,372742,248054) : difference with theory (-35) = 0 CORRECTING DEFECT 11 (vertices=86, convex hull=101, v0=18798) After retessellation of defect 11 (v0=18798), euler #=-34 (124690,372891,248167) : difference with theory (-34) = 0 CORRECTING DEFECT 12 (vertices=35, convex hull=75, v0=23275) After retessellation of defect 12 (v0=23275), euler #=-33 (124715,372997,248249) : difference with theory (-33) = 0 CORRECTING DEFECT 13 (vertices=88, convex hull=110, v0=25872) After retessellation of defect 13 (v0=25872), euler #=-32 (124757,373174,248385) : difference with theory (-32) = 0 CORRECTING DEFECT 14 (vertices=67, convex hull=43, v0=26213) After retessellation of defect 14 (v0=26213), euler #=-31 (124764,373212,248417) : difference with theory (-31) = 0 CORRECTING DEFECT 15 (vertices=86, convex hull=86, v0=35165) After retessellation of defect 15 (v0=35165), euler #=-30 (124802,373365,248533) : difference with theory (-30) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=31, v0=36941) After retessellation of defect 16 (v0=36941), euler #=-29 (124806,373388,248553) : difference with theory (-29) = 0 CORRECTING DEFECT 17 (vertices=99, convex hull=110, v0=46867) After retessellation of defect 17 (v0=46867), euler #=-28 (124850,373573,248695) : difference with theory (-28) = 0 CORRECTING DEFECT 18 (vertices=216, convex hull=97, v0=51128) After retessellation of defect 18 (v0=51128), euler #=-27 (124887,373729,248815) : difference with theory (-27) = 0 CORRECTING DEFECT 19 (vertices=40, convex hull=73, v0=55511) After retessellation of defect 19 (v0=55511), euler #=-26 (124914,373839,248899) : difference with theory (-26) = 0 CORRECTING DEFECT 20 (vertices=20, convex hull=21, v0=57050) After retessellation of defect 20 (v0=57050), euler #=-25 (124917,373856,248914) : difference with theory (-25) = 0 CORRECTING DEFECT 21 (vertices=85, convex hull=89, v0=59884) After retessellation of defect 21 (v0=59884), euler #=-24 (124944,373979,249011) : difference with theory (-24) = 0 CORRECTING DEFECT 22 (vertices=226, convex hull=168, v0=60691) After retessellation of defect 22 (v0=60691), euler #=-23 (125004,374237,249210) : difference with theory (-23) = 0 CORRECTING DEFECT 23 (vertices=20, convex hull=25, v0=68057) After retessellation of defect 23 (v0=68057), euler #=-22 (125009,374259,249228) : difference with theory (-22) = 0 CORRECTING DEFECT 24 (vertices=123, convex hull=46, v0=73747) After retessellation of defect 24 (v0=73747), euler #=-21 (125023,374317,249273) : difference with theory (-21) = 0 CORRECTING DEFECT 25 (vertices=37, convex hull=45, v0=83856) After retessellation of defect 25 (v0=83856), euler #=-20 (125027,374345,249298) : difference with theory (-20) = 0 CORRECTING DEFECT 26 (vertices=47, convex hull=79, v0=89152) After retessellation of defect 26 (v0=89152), euler #=-19 (125036,374404,249349) : difference with theory (-19) = 0 CORRECTING DEFECT 27 (vertices=31, convex hull=46, v0=92707) After retessellation of defect 27 (v0=92707), euler #=-18 (125055,374472,249399) : difference with theory (-18) = 0 CORRECTING DEFECT 28 (vertices=33, convex hull=68, v0=92994) After retessellation of defect 28 (v0=92994), euler #=-17 (125073,374556,249466) : difference with theory (-17) = 0 CORRECTING DEFECT 29 (vertices=331, convex hull=73, v0=96584) After retessellation of defect 29 (v0=96584), euler #=-16 (125093,374648,249539) : difference with theory (-16) = 0 CORRECTING DEFECT 30 (vertices=506, convex hull=207, v0=96669) After retessellation of defect 30 (v0=96669), euler #=-15 (125169,374986,249802) : difference with theory (-15) = 0 CORRECTING DEFECT 31 (vertices=116, convex hull=70, v0=97612) After retessellation of defect 31 (v0=97612), euler #=-14 (125178,375040,249848) : difference with theory (-14) = 0 CORRECTING DEFECT 32 (vertices=12, convex hull=27, v0=99413) After retessellation of defect 32 (v0=99413), euler #=-13 (125180,375055,249862) : difference with theory (-13) = 0 CORRECTING DEFECT 33 (vertices=63, convex hull=72, v0=100203) After retessellation of defect 33 (v0=100203), euler #=-12 (125209,375173,249952) : difference with theory (-12) = 0 CORRECTING DEFECT 34 (vertices=82, convex hull=122, v0=104288) After retessellation of defect 34 (v0=104288), euler #=-11 (125253,375354,250090) : difference with theory (-11) = 0 CORRECTING DEFECT 35 (vertices=188, convex hull=90, v0=104948) After retessellation of defect 35 (v0=104948), euler #=-10 (125278,375470,250182) : difference with theory (-10) = 0 CORRECTING DEFECT 36 (vertices=191, convex hull=79, v0=105190) After retessellation of defect 36 (v0=105190), euler #=-9 (125308,375595,250278) : difference with theory (-9) = 0 CORRECTING DEFECT 37 (vertices=41, convex hull=62, v0=106093) After retessellation of defect 37 (v0=106093), euler #=-8 (125327,375679,250344) : difference with theory (-8) = 0 CORRECTING DEFECT 38 (vertices=107, convex hull=111, v0=108443) After retessellation of defect 38 (v0=108443), euler #=-7 (125347,375792,250438) : difference with theory (-7) = 0 CORRECTING DEFECT 39 (vertices=92, convex hull=33, v0=110799) After retessellation of defect 39 (v0=110799), euler #=-6 (125350,375817,250461) : difference with theory (-6) = 0 CORRECTING DEFECT 40 (vertices=47, convex hull=83, v0=111705) After retessellation of defect 40 (v0=111705), euler #=-5 (125368,375909,250536) : difference with theory (-5) = 0 CORRECTING DEFECT 41 (vertices=22, convex hull=65, v0=114840) After retessellation of defect 41 (v0=114840), euler #=-4 (125375,375955,250576) : difference with theory (-4) = 0 CORRECTING DEFECT 42 (vertices=62, convex hull=36, v0=116278) After retessellation of defect 42 (v0=116278), euler #=-3 (125383,375993,250607) : difference with theory (-3) = 0 CORRECTING DEFECT 43 (vertices=32, convex hull=77, v0=122447) After retessellation of defect 43 (v0=122447), euler #=-2 (125399,376070,250669) : difference with theory (-2) = 0 CORRECTING DEFECT 44 (vertices=33, convex hull=27, v0=123772) After retessellation of defect 44 (v0=123772), euler #=-1 (125401,376086,250684) : difference with theory (-1) = 0 CORRECTING DEFECT 45 (vertices=95, convex hull=129, v0=125895) After retessellation of defect 45 (v0=125895), euler #=0 (125432,376236,250804) : difference with theory (0) = 0 CORRECTING DEFECT 46 (vertices=57, convex hull=103, v0=126630) After retessellation of defect 46 (v0=126630), euler #=1 (125462,376369,250908) : difference with theory (1) = 0 CORRECTING DEFECT 47 (vertices=14, convex hull=31, v0=128426) After retessellation of defect 47 (v0=128426), euler #=2 (125464,376386,250924) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->9.05) (max @ vno 59464 --> 63269) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->9.05) (max @ vno 59464 --> 63269) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 136 mutations (31.7%), 293 crossovers (68.3%), 146 vertices were eliminated building final representation... 3102 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125464, nf=250924, ne=376386, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 24.1 minutes 0 defective edges removing intersecting faces 000: 273 intersecting 001: 21 intersecting mris_fix_topology utimesec 1445.988176 mris_fix_topology stimesec 0.273958 mris_fix_topology ru_maxrss 410432 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 53990 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 7680 mris_fix_topology ru_oublock 12088 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 331 mris_fix_topology ru_nivcsw 9722 FSRUNTIME@ mris_fix_topology rh 0.4022 hours 1 threads PIDs (8933 8936) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 121292 - 363870 + 242580 = 2 --> 0 holes F =2V-4: 242580 = 242584-4 (0) 2E=3F: 727740 = 727740 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 125464 - 376386 + 250924 = 2 --> 0 holes F =2V-4: 250924 = 250928-4 (0) 2E=3F: 752772 = 752772 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 244 intersecting 001: 8 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 13 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Oct 8 09:11:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 lh #-------------------------------------------- #@# Make White Surf rh Sun Oct 8 09:11:23 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 rh Waiting for PID 19846 of (19846 19849) to complete... Waiting for PID 19849 of (19846 19849) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... 12664 bright wm thresholded. 2174 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.orig... computing class statistics... border white: 240984 voxels (1.44%) border gray 284361 voxels (1.69%) WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0] GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.4 (was 70) setting MAX_BORDER_WHITE to 109.6 (was 105) setting MIN_BORDER_WHITE to 65.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 92.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.84 +- 0.24 (0.03-->4.97) (max @ vno 7895 --> 119426) face area 0.29 +- 0.14 (0.00-->5.27) mean absolute distance = 0.62 +- 0.73 3485 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=101+-7.0, GM=65+-7.0 mean inside = 91.4, mean outside = 73.7 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 mean border=77.7, 89 (89) missing vertices, mean dist 0.3 [0.4 (%33.6)->0.7 (%66.4))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.13-->4.83) (max @ vno 120250 --> 120298) face area 0.29 +- 0.15 (0.00-->4.35) mean absolute distance = 0.29 +- 0.51 2361 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2784216.2, rms=9.905 001: dt: 0.5000, sse=1638215.8, rms=7.009 (29.231%) 002: dt: 0.5000, sse=1146538.2, rms=5.294 (24.473%) 003: dt: 0.5000, sse=918095.4, rms=4.261 (19.505%) 004: dt: 0.5000, sse=815291.6, rms=3.709 (12.973%) 005: dt: 0.5000, sse=782778.9, rms=3.439 (7.275%) 006: dt: 0.5000, sse=753442.6, rms=3.318 (3.502%) 007: dt: 0.5000, sse=743844.2, rms=3.256 (1.875%) rms = 3.22, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=739923.2, rms=3.224 (1.000%) 009: dt: 0.2500, sse=596442.7, rms=1.929 (40.155%) 010: dt: 0.2500, sse=574940.8, rms=1.654 (14.259%) 011: dt: 0.2500, sse=570057.6, rms=1.584 (4.250%) rms = 1.55, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=567648.5, rms=1.546 (2.398%) rms = 1.50, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=564331.2, rms=1.500 (2.957%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 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 mean border=79.8, 117 (43) missing vertices, mean dist -0.1 [0.3 (%69.3)->0.3 (%30.7))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.26 (0.10-->4.86) (max @ vno 14221 --> 119427) face area 0.36 +- 0.18 (0.00-->5.58) mean absolute distance = 0.25 +- 0.41 2591 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=954143.4, rms=3.712 014: dt: 0.5000, sse=774203.7, rms=2.447 (34.078%) rms = 2.65, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=709294.1, rms=1.795 (26.654%) 016: dt: 0.2500, sse=683722.0, rms=1.446 (19.452%) 017: dt: 0.2500, sse=677159.2, rms=1.340 (7.320%) rms = 1.31, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=674556.2, rms=1.308 (2.371%) rms = 1.27, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=674501.4, rms=1.273 (2.666%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.4, 118 (39) missing vertices, mean dist -0.1 [0.3 (%63.8)->0.2 (%36.2))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.26 (0.05-->4.95) (max @ vno 120883 --> 91955) face area 0.36 +- 0.18 (0.00-->5.71) mean absolute distance = 0.24 +- 0.36 2509 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=772011.7, rms=2.477 020: dt: 0.5000, sse=753286.9, rms=2.252 (9.078%) rms = 2.54, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=691038.1, rms=1.537 (31.774%) 022: dt: 0.2500, sse=677510.9, rms=1.242 (19.161%) 023: dt: 0.2500, sse=661213.2, rms=1.170 (5.834%) rms = 1.16, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=660185.1, rms=1.163 (0.576%) rms = 1.13, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=657667.4, rms=1.134 (2.512%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.1, 130 (38) missing vertices, mean dist -0.0 [0.3 (%54.4)->0.2 (%45.6))] %86 local maxima, % 8 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-6.0.0/0050566/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=670070.2, rms=1.444 rms = 1.49, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=649025.1, rms=1.086 (24.823%) 027: dt: 0.2500, sse=645450.9, rms=0.894 (17.656%) rms = 0.89, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=642983.0, rms=0.891 (0.395%) rms = 0.89, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=642777.4, rms=0.886 (0.541%) positioning took 0.4 minutes generating cortex label... 10 non-cortical segments detected only using segment with 7382 vertices erasing segment 0 (vno[0] = 32688) erasing segment 1 (vno[0] = 32720) erasing segment 2 (vno[0] = 33594) erasing segment 3 (vno[0] = 37419) erasing segment 4 (vno[0] = 38419) erasing segment 6 (vno[0] = 88196) erasing segment 7 (vno[0] = 88295) erasing segment 8 (vno[0] = 90067) erasing segment 9 (vno[0] = 120851) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.area vertex spacing 0.92 +- 0.27 (0.03-->5.05) (max @ vno 91955 --> 120883) face area 0.35 +- 0.18 (0.00-->5.79) refinement took 4.3 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... 12664 bright wm thresholded. 2174 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.orig... computing class statistics... border white: 240984 voxels (1.44%) border gray 284361 voxels (1.69%) WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0] GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 53.4 (was 70) setting MAX_BORDER_WHITE to 109.6 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 42.9 (was 40) setting MAX_GRAY to 92.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.03-->3.43) (max @ vno 64931 --> 66846) face area 0.29 +- 0.12 (0.00-->2.27) mean absolute distance = 0.62 +- 0.72 4110 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=101+-7.0, GM=64+-8.7 mean inside = 91.7, mean outside = 73.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=77.5, 60 (60) missing vertices, mean dist 0.4 [0.4 (%31.4)->0.7 (%68.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.08-->3.65) (max @ vno 124624 --> 124652) face area 0.29 +- 0.13 (0.00-->2.44) mean absolute distance = 0.28 +- 0.48 2851 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2996296.2, rms=10.166 001: dt: 0.5000, sse=1757392.4, rms=7.227 (28.911%) 002: dt: 0.5000, sse=1205797.8, rms=5.414 (25.089%) 003: dt: 0.5000, sse=949113.4, rms=4.320 (20.199%) 004: dt: 0.5000, sse=838049.2, rms=3.741 (13.416%) 005: dt: 0.5000, sse=791101.1, rms=3.464 (7.385%) 006: dt: 0.5000, sse=771127.3, rms=3.331 (3.852%) 007: dt: 0.5000, sse=760110.4, rms=3.263 (2.030%) rms = 3.22, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=754191.6, rms=3.225 (1.183%) 009: dt: 0.2500, sse=602436.1, rms=1.886 (41.514%) 010: dt: 0.2500, sse=579271.2, rms=1.598 (15.264%) 011: dt: 0.2500, sse=573103.2, rms=1.517 (5.093%) rms = 1.47, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=570230.2, rms=1.474 (2.847%) 013: dt: 0.1250, sse=566874.5, rms=1.420 (3.643%) rms = 1.41, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=566209.9, rms=1.410 (0.696%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... mean border=79.7, 44 (4) missing vertices, mean dist -0.1 [0.3 (%69.0)->0.3 (%31.0))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.25 (0.10-->3.91) (max @ vno 124624 --> 124652) face area 0.36 +- 0.16 (0.00-->2.83) mean absolute distance = 0.25 +- 0.40 3382 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=982169.1, rms=3.747 015: dt: 0.5000, sse=788934.2, rms=2.456 (34.448%) rms = 2.64, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=720692.5, rms=1.779 (27.578%) 017: dt: 0.2500, sse=693278.5, rms=1.386 (22.067%) 018: dt: 0.2500, sse=682687.3, rms=1.251 (9.761%) rms = 1.21, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=680249.5, rms=1.210 (3.311%) rms = 1.17, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=678136.2, rms=1.171 (3.189%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.3, 40 (2) missing vertices, mean dist -0.1 [0.3 (%64.1)->0.2 (%35.9))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.24 (0.09-->3.89) (max @ vno 124624 --> 124652) face area 0.35 +- 0.16 (0.00-->2.75) mean absolute distance = 0.25 +- 0.36 2729 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=793674.1, rms=2.547 021: dt: 0.5000, sse=759713.2, rms=2.258 (11.351%) rms = 2.51, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=694395.1, rms=1.533 (32.101%) 023: dt: 0.2500, sse=672469.6, rms=1.199 (21.778%) 024: dt: 0.2500, sse=666716.6, rms=1.100 (8.285%) rms = 1.09, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=665669.7, rms=1.085 (1.318%) rms = 1.05, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=664011.6, rms=1.053 (3.019%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.0, 55 (1) missing vertices, mean dist -0.0 [0.3 (%55.0)->0.2 (%45.0))] %86 local maxima, % 9 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-6.0.0/0050566/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=682505.8, rms=1.463 rms = 1.45, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=680687.2, rms=1.454 (0.618%) 028: dt: 0.2500, sse=655120.9, rms=1.024 (29.582%) 029: dt: 0.2500, sse=648259.6, rms=0.895 (12.595%) rms = 0.94, time step reduction 2 of 3 to 0.125... rms = 0.86, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=646584.3, rms=0.857 (4.162%) positioning took 0.4 minutes generating cortex label... 3 non-cortical segments detected only using segment with 7628 vertices erasing segment 0 (vno[0] = 37911) erasing segment 2 (vno[0] = 91649) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.area vertex spacing 0.91 +- 0.25 (0.03-->3.58) (max @ vno 124624 --> 124652) face area 0.35 +- 0.16 (0.00-->2.61) refinement took 4.6 minutes PIDs (19846 19849) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun Oct 8 09:15:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun Oct 8 09:15:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 20022 of (20022 20025) to complete... Waiting for PID 20025 of (20022 20025) 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 (20022 20025) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun Oct 8 09:16:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun Oct 8 09:16:03 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 20070 of (20070 20073) to complete... Waiting for PID 20073 of (20070 20073) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.4 mm, total surface area = 77743 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 38.736111 mris_inflate stimesec 0.100984 mris_inflate ru_maxrss 178024 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 26182 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9504 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5761 mris_inflate ru_nivcsw 4239 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.9 mm, total surface area = 79613 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.028 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 39.868939 mris_inflate stimesec 0.107983 mris_inflate ru_maxrss 183620 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 27070 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9832 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 4565 mris_inflate ru_nivcsw 4844 PIDs (20070 20073) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun Oct 8 09:16:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 09:16:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 20177 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20180 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20183 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20186 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20189 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20192 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20195 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20198 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20201 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20204 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20207 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... Waiting for PID 20211 of (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 13.746*4pi (172.736) --> -13 handles ICI = 149.1, FI = 1418.6, variation=22634.810 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 138 vertices thresholded to be in k1 ~ [-0.28 0.39], k2 ~ [-0.13 0.07] total integrated curvature = 0.365*4pi (4.581) --> 1 handles ICI = 1.2, FI = 8.1, variation=139.504 100 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 124 vertices thresholded to be in [-0.16 0.18] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = 20.324*4pi (255.397) --> -19 handles ICI = 151.5, FI = 1462.2, variation=23131.480 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 162 vertices thresholded to be in k1 ~ [-0.30 0.79], k2 ~ [-0.24 0.16] total integrated curvature = 0.419*4pi (5.261) --> 1 handles ICI = 1.4, FI = 8.8, variation=151.127 119 vertices thresholded to be in [-0.07 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 106 vertices thresholded to be in [-0.16 0.22] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023 done. PIDs (20177 20180 20183 20186 20189 20192 20195 20198 20201 20204 20207 20211) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun Oct 8 09:17:58 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050566 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 [ 0050566/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 [ 230 ] Gb_filter = 0 WARN: S lookup min: -0.358928 WARN: S explicit min: 0.000000 vertex = 2260 #----------------------------------------- #@# Curvature Stats rh Sun Oct 8 09:18:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050566 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 [ 0050566/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 [ 254 ] Gb_filter = 0 WARN: S lookup min: -0.267072 WARN: S explicit min: 0.000000 vertex = 1250 #-------------------------------------------- #@# Sphere lh Sun Oct 8 09:18:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun Oct 8 09:18:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 20350 of (20350 20353) to complete... Waiting for PID 20353 of (20350 20353) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0.304... 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 %43.79 pass 1: epoch 2 of 3 starting distance error %21.42 unfolding complete - removing small folds... starting distance error %21.13 removing remaining folds... final distance error %21.16 MRISunfold() return, current seed 1234 -01: dt=0.0000, 30 negative triangles 186: dt=0.9900, 30 negative triangles 187: dt=0.9900, 10 negative triangles 188: dt=0.9900, 9 negative triangles 189: dt=0.9900, 8 negative triangles 190: dt=0.9900, 6 negative triangles 191: dt=0.9900, 6 negative triangles 192: dt=0.9900, 2 negative triangles 193: dt=0.9900, 3 negative triangles 194: dt=0.9900, 2 negative triangles 195: dt=0.9900, 4 negative triangles 196: dt=0.9900, 6 negative triangles 197: dt=0.9900, 4 negative triangles 198: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.55 hours mris_sphere utimesec 1969.463596 mris_sphere stimesec 0.831873 mris_sphere ru_maxrss 250072 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 44834 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8568 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 91506 mris_sphere ru_nivcsw 162004 FSRUNTIME@ mris_sphere 0.5476 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0.301... 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 %21.23 pass 1: epoch 2 of 3 starting distance error %21.16 unfolding complete - removing small folds... starting distance error %21.03 removing remaining folds... final distance error %21.07 MRISunfold() return, current seed 1234 -01: dt=0.0000, 52 negative triangles 235: dt=0.9900, 52 negative triangles 236: dt=0.9900, 26 negative triangles 237: dt=0.9900, 17 negative triangles 238: dt=0.9900, 20 negative triangles 239: dt=0.9900, 13 negative triangles 240: dt=0.9900, 12 negative triangles 241: dt=0.9900, 17 negative triangles 242: dt=0.9900, 13 negative triangles 243: dt=0.9900, 13 negative triangles 244: dt=0.9900, 12 negative triangles 245: dt=0.9900, 5 negative triangles 246: dt=0.9900, 10 negative triangles 247: dt=0.9900, 10 negative triangles 248: dt=0.9900, 8 negative triangles 249: dt=0.9900, 8 negative triangles 250: dt=0.9900, 8 negative triangles 251: dt=0.9900, 8 negative triangles 252: dt=0.9900, 3 negative triangles 253: dt=0.9900, 6 negative triangles 254: dt=0.9900, 4 negative triangles 255: dt=0.9900, 7 negative triangles 256: dt=0.9900, 2 negative triangles 257: dt=0.9900, 5 negative triangles 258: dt=0.9900, 5 negative triangles 259: dt=0.9900, 5 negative triangles 260: dt=0.9900, 3 negative triangles 261: dt=0.9900, 7 negative triangles 262: dt=0.9900, 5 negative triangles 263: dt=0.9900, 2 negative triangles 264: dt=0.9900, 2 negative triangles 265: dt=0.9900, 2 negative triangles 266: dt=0.9405, 5 negative triangles 267: dt=0.9405, 2 negative triangles 268: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.75 hours mris_sphere utimesec 3319.245398 mris_sphere stimesec 1.165822 mris_sphere ru_maxrss 258568 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 45927 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8864 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 109825 mris_sphere ru_nivcsw 165902 FSRUNTIME@ mris_sphere 0.7496 hours 1 threads PIDs (20350 20353) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sun Oct 8 10:03:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 10:03:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 22035 of (22035 22038) to complete... Waiting for PID 22038 of (22035 22038) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 5.738 curvature mean = 0.040, std = 0.821 curvature mean = 0.008, std = 0.875 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 301173.9, tmin=0.9338 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 209498.0, tmin=1.8855 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 202056.6, tmin=2.8476 d=8.00 min @ (2.00, 2.00, 0.00) sse = 193921.5, tmin=3.8146 d=4.00 min @ (0.00, -1.00, -1.00) sse = 192118.0, tmin=4.7899 d=2.00 min @ (0.00, 0.50, 0.00) sse = 192070.1, tmin=5.7718 d=1.00 min @ (0.00, -0.25, 0.00) sse = 192000.1, tmin=6.7522 d=0.50 min @ (0.12, 0.00, -0.12) sse = 191972.3, tmin=7.7332 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 7.73 min curvature mean = 0.009, std = 0.835 curvature mean = 0.003, std = 0.954 curvature mean = 0.007, std = 0.846 curvature mean = 0.002, std = 0.982 curvature mean = 0.006, std = 0.849 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.030, std = 0.265 curvature mean = 0.043, std = 0.246 curvature mean = 0.049, std = 0.406 curvature mean = 0.037, std = 0.305 curvature mean = 0.037, std = 0.583 curvature mean = 0.036, std = 0.332 curvature mean = 0.020, std = 0.722 curvature mean = 0.036, std = 0.343 curvature mean = 0.007, std = 0.825 MRISregister() return, current seed 0 -01: dt=0.0000, 42 negative triangles 111: dt=0.9900, 42 negative triangles expanding nbhd size to 1 112: dt=0.9900, 55 negative triangles 113: dt=0.9900, 27 negative triangles 114: dt=0.9900, 27 negative triangles 115: dt=0.9900, 22 negative triangles 116: dt=0.9900, 24 negative triangles 117: dt=0.9900, 19 negative triangles 118: dt=0.9900, 15 negative triangles 119: dt=0.9900, 16 negative triangles 120: dt=0.9900, 15 negative triangles 121: dt=0.9900, 10 negative triangles 122: dt=0.9900, 11 negative triangles 123: dt=0.9900, 10 negative triangles 124: dt=0.9900, 8 negative triangles 125: dt=0.9900, 5 negative triangles 126: dt=0.9900, 4 negative triangles 127: dt=0.9900, 6 negative triangles 128: dt=0.9900, 3 negative triangles 129: dt=0.9900, 3 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.04 hours mris_register utimesec 3757.921709 mris_register stimesec 2.764579 mris_register ru_maxrss 233232 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 33233 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 8632 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 329895 mris_register ru_nivcsw 201008 FSRUNTIME@ mris_register 1.0444 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 5.803 curvature mean = 0.035, std = 0.814 curvature mean = 0.007, std = 0.876 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 306683.7, tmin=0.9667 d=32.00 min @ (8.00, 8.00, 0.00) sse = 196065.8, tmin=1.9505 d=8.00 min @ (0.00, 0.00, 2.00) sse = 191396.3, tmin=3.9429 d=4.00 min @ (1.00, 0.00, -1.00) sse = 190387.2, tmin=4.9432 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 189694.4, tmin=5.9531 d=1.00 min @ (0.00, -0.25, -0.25) sse = 189452.9, tmin=6.9660 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 189428.7, tmin=7.9993 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 8.00 min curvature mean = 0.025, std = 0.833 curvature mean = 0.002, std = 0.955 curvature mean = 0.024, std = 0.845 curvature mean = 0.001, std = 0.982 curvature mean = 0.023, std = 0.848 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.030, std = 0.264 curvature mean = 0.041, std = 0.240 curvature mean = 0.049, std = 0.405 curvature mean = 0.034, std = 0.300 curvature mean = 0.037, std = 0.587 curvature mean = 0.033, std = 0.327 curvature mean = 0.019, std = 0.725 curvature mean = 0.032, std = 0.339 curvature mean = 0.006, std = 0.823 MRISregister() return, current seed 0 -01: dt=0.0000, 75 negative triangles 113: dt=0.9900, 75 negative triangles expanding nbhd size to 1 114: dt=0.9900, 87 negative triangles 115: dt=0.9900, 73 negative triangles 116: dt=0.9900, 68 negative triangles 117: dt=0.9900, 72 negative triangles 118: dt=0.9900, 61 negative triangles 119: dt=0.9900, 56 negative triangles 120: dt=0.9900, 55 negative triangles 121: dt=0.9900, 54 negative triangles 122: dt=0.9900, 45 negative triangles 123: dt=0.9900, 43 negative triangles 124: dt=0.9900, 37 negative triangles 125: dt=0.9900, 35 negative triangles 126: dt=0.9900, 32 negative triangles 127: dt=0.9900, 35 negative triangles 128: dt=0.9900, 28 negative triangles 129: dt=0.9900, 28 negative triangles 130: dt=0.9900, 27 negative triangles 131: dt=0.9900, 22 negative triangles 132: dt=0.9900, 23 negative triangles 133: dt=0.9900, 22 negative triangles 134: dt=0.9900, 16 negative triangles 135: dt=0.9900, 14 negative triangles 136: dt=0.9900, 14 negative triangles 137: dt=0.9900, 12 negative triangles 138: dt=0.9900, 11 negative triangles 139: dt=0.9900, 13 negative triangles 140: dt=0.9900, 12 negative triangles 141: dt=0.9900, 10 negative triangles 142: dt=0.9900, 9 negative triangles 143: dt=0.9900, 8 negative triangles 144: dt=0.9900, 12 negative triangles 145: dt=0.9900, 7 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 7 negative triangles 149: dt=0.9900, 7 negative triangles 150: dt=0.9900, 4 negative triangles 151: dt=0.9900, 5 negative triangles 152: dt=0.9900, 4 negative triangles 153: dt=0.9900, 5 negative triangles 154: dt=0.9900, 2 negative triangles 155: dt=0.9900, 1 negative triangles 156: dt=0.9900, 5 negative triangles 157: dt=0.9900, 3 negative triangles 158: dt=0.9900, 2 negative triangles 159: dt=0.9900, 1 negative triangles 160: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.15 hours mris_register utimesec 4353.764127 mris_register stimesec 2.722586 mris_register ru_maxrss 238168 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 34759 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 8832 mris_register ru_oublock 8920 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 353905 mris_register ru_nivcsw 204788 FSRUNTIME@ mris_register 1.1528 hours 1 threads PIDs (22035 22038) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sun Oct 8 11:12:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sun Oct 8 11:12:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 24617 of (24617 24620) to complete... Waiting for PID 24620 of (24617 24620) 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 (24617 24620) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sun Oct 8 11:12:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 11:12:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 24665 of (24665 24668) to complete... Waiting for PID 24668 of (24665 24668) 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 (24665 24668) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sun Oct 8 11:12:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 11:12:18 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 24710 of (24710 24713) to complete... Waiting for PID 24713 of (24710 24713) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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... 954 labels changed using aseg relabeling using gibbs priors... 000: 2741 changed, 121292 examined... 001: 629 changed, 11432 examined... 002: 125 changed, 3537 examined... 003: 42 changed, 778 examined... 004: 13 changed, 253 examined... 005: 7 changed, 81 examined... 006: 2 changed, 44 examined... 007: 2 changed, 14 examined... 008: 1 changed, 11 examined... 009: 0 changed, 5 examined... 191 labels changed using aseg 000: 105 total segments, 59 labels (215 vertices) changed 001: 43 total segments, 3 labels (6 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1230 vertices marked for relabeling... 1230 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 13 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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... 982 labels changed using aseg relabeling using gibbs priors... 000: 2591 changed, 125464 examined... 001: 595 changed, 11415 examined... 002: 117 changed, 3319 examined... 003: 50 changed, 747 examined... 004: 18 changed, 306 examined... 005: 7 changed, 107 examined... 006: 7 changed, 51 examined... 007: 1 changed, 33 examined... 008: 0 changed, 7 examined... 163 labels changed using aseg 000: 95 total segments, 58 labels (202 vertices) changed 001: 39 total segments, 2 labels (2 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1066 vertices marked for relabeling... 1066 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. PIDs (24710 24713) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sun Oct 8 11:12:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 lh #-------------------------------------------- #@# Make Pial Surf rh Sun Oct 8 11:12:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 rh Waiting for PID 24766 of (24766 24769) to complete... Waiting for PID 24769 of (24766 24769) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... 12664 bright wm thresholded. 2174 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.orig... computing class statistics... border white: 240984 voxels (1.44%) border gray 284361 voxels (1.69%) WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0] GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.4 (was 70) setting MAX_BORDER_WHITE to 109.6 (was 105) setting MIN_BORDER_WHITE to 65.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 92.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-7.0, GM=65+-7.0 mean inside = 91.4, mean outside = 73.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.27 (0.03-->5.05) (max @ vno 91955 --> 120883) face area 0.35 +- 0.18 (0.00-->5.75) mean absolute distance = 0.44 +- 0.69 2261 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 90 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 160 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 35 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown deleting segment 14 with 19 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown mean border=77.2, 101 (100) missing vertices, mean dist 0.3 [0.5 (%17.5)->0.4 (%82.5))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.28 (0.11-->5.51) (max @ vno 120883 --> 91955) face area 0.35 +- 0.18 (0.00-->5.21) mean absolute distance = 0.29 +- 0.54 2255 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1621828.2, rms=6.576 001: dt: 0.5000, sse=970163.8, rms=3.904 (40.632%) 002: dt: 0.5000, sse=833555.8, rms=3.082 (21.069%) 003: dt: 0.5000, sse=825576.4, rms=3.031 (1.630%) 004: dt: 0.5000, sse=807652.2, rms=2.910 (4.004%) rms = 3.03, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=715992.2, rms=2.058 (29.265%) 006: dt: 0.2500, sse=686215.2, rms=1.676 (18.570%) 007: dt: 0.2500, sse=678197.9, rms=1.577 (5.893%) rms = 1.56, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=677294.4, rms=1.556 (1.330%) rms = 1.52, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=677685.2, rms=1.523 (2.112%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 1 with 99 points - only 0.00% unknown deleting segment 2 with 18 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 108 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 53 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown mean border=79.6, 120 (64) missing vertices, mean dist -0.2 [0.3 (%70.5)->0.2 (%29.5))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.27 (0.07-->5.62) (max @ vno 120883 --> 91955) face area 0.37 +- 0.19 (0.00-->5.56) mean absolute distance = 0.25 +- 0.43 2481 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=974661.2, rms=3.712 010: dt: 0.5000, sse=783132.2, rms=2.380 (35.879%) rms = 2.57, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=725141.4, rms=1.747 (26.608%) 012: dt: 0.2500, sse=698320.5, rms=1.398 (19.951%) 013: dt: 0.2500, sse=691907.8, rms=1.296 (7.318%) rms = 1.27, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=690368.8, rms=1.271 (1.949%) rms = 1.24, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=688785.7, rms=1.242 (2.261%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 1 with 113 points - only 0.00% unknown deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 106 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 53 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=81.3, 127 (59) missing vertices, mean dist -0.1 [0.3 (%64.2)->0.2 (%35.8))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.27 (0.10-->5.78) (max @ vno 120883 --> 91955) face area 0.36 +- 0.19 (0.00-->5.63) mean absolute distance = 0.25 +- 0.37 2431 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=782290.3, rms=2.492 016: dt: 0.5000, sse=754797.3, rms=2.233 (10.391%) rms = 2.50, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=692352.2, rms=1.519 (31.989%) 018: dt: 0.2500, sse=674258.9, rms=1.219 (19.746%) 019: dt: 0.2500, sse=668790.6, rms=1.152 (5.506%) rms = 1.15, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=668469.5, rms=1.148 (0.301%) rms = 1.12, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=666976.9, rms=1.123 (2.195%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 108 points - only 0.00% unknown deleting segment 2 with 21 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 113 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 53 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=82.0, 146 (55) missing vertices, mean dist -0.0 [0.3 (%54.6)->0.2 (%45.4))] %87 local maxima, % 8 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-6.0.0/0050566/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=677431.0, rms=1.432 rms = 1.49, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=656268.9, rms=1.063 (25.793%) 023: dt: 0.2500, sse=648780.9, rms=0.870 (18.177%) rms = 0.87, time step reduction 2 of 3 to 0.125... rms = 0.87, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=647529.4, rms=0.868 (0.226%) positioning took 0.4 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7396 vertices erasing segment 0 (vno[0] = 33594) erasing segment 1 (vno[0] = 34474) erasing segment 3 (vno[0] = 88196) erasing segment 4 (vno[0] = 88295) erasing segment 5 (vno[0] = 90067) erasing segment 6 (vno[0] = 120851) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.area vertex spacing 0.92 +- 0.27 (0.03-->5.79) (max @ vno 91955 --> 120883) face area 0.36 +- 0.19 (0.00-->5.71) 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 29 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=53.0, 107 (107) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.7 (%100.0))] % 9 local maxima, %48 large gradients and %38 min vals, 887 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=20769124.0, rms=29.574 001: dt: 0.0500, sse=18332574.0, rms=27.728 (6.241%) 002: dt: 0.0500, sse=16579036.0, rms=26.320 (5.079%) 003: dt: 0.0500, sse=15227909.0, rms=25.181 (4.327%) 004: dt: 0.0500, sse=14127705.0, rms=24.214 (3.841%) 005: dt: 0.0500, sse=13195252.0, rms=23.363 (3.515%) 006: dt: 0.0500, sse=12384146.0, rms=22.596 (3.281%) 007: dt: 0.0500, sse=11662920.0, rms=21.892 (3.116%) 008: dt: 0.0500, sse=11012877.0, rms=21.237 (2.991%) 009: dt: 0.0500, sse=10420728.0, rms=20.623 (2.894%) 010: dt: 0.0500, sse=9877192.0, rms=20.042 (2.816%) positioning took 0.8 minutes mean border=52.9, 110 (73) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.2 (%100.0))] %10 local maxima, %47 large gradients and %38 min vals, 850 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=10474192.0, rms=20.678 011: dt: 0.0500, sse=9968826.0, rms=20.140 (2.601%) 012: dt: 0.0500, sse=9499765.0, rms=19.627 (2.545%) 013: dt: 0.0500, sse=9063099.0, rms=19.138 (2.494%) 014: dt: 0.0500, sse=8656216.0, rms=18.670 (2.444%) 015: dt: 0.0500, sse=8276600.0, rms=18.222 (2.396%) 016: dt: 0.0500, sse=7922216.5, rms=17.795 (2.348%) 017: dt: 0.0500, sse=7591744.0, rms=17.386 (2.296%) 018: dt: 0.0500, sse=7283855.5, rms=16.996 (2.241%) 019: dt: 0.0500, sse=6996662.0, rms=16.624 (2.188%) 020: dt: 0.0500, sse=6728686.0, rms=16.270 (2.134%) positioning took 0.8 minutes mean border=52.7, 101 (57) missing vertices, mean dist 1.2 [0.1 (%0.8)->1.9 (%99.2))] %10 local maxima, %47 large gradients and %38 min vals, 852 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=6819666.0, rms=16.395 021: dt: 0.0500, sse=6564234.5, rms=16.052 (2.091%) 022: dt: 0.0500, sse=6326888.5, rms=15.727 (2.027%) 023: dt: 0.0500, sse=6105191.0, rms=15.416 (1.973%) 024: dt: 0.0500, sse=5899113.5, rms=15.122 (1.909%) 025: dt: 0.0500, sse=5707338.0, rms=14.843 (1.846%) 026: dt: 0.0500, sse=5528651.5, rms=14.578 (1.786%) 027: dt: 0.0500, sse=5361297.0, rms=14.325 (1.734%) 028: dt: 0.0500, sse=5203107.0, rms=14.082 (1.698%) 029: dt: 0.0500, sse=5053418.0, rms=13.847 (1.664%) 030: dt: 0.0500, sse=4911743.0, rms=13.622 (1.629%) positioning took 0.8 minutes mean border=52.7, 122 (50) missing vertices, mean dist 1.0 [0.1 (%12.1)->1.8 (%87.9))] %10 local maxima, %48 large gradients and %37 min vals, 847 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=4969178.0, rms=13.712 031: dt: 0.5000, sse=3990408.2, rms=12.051 (12.109%) 032: dt: 0.5000, sse=3364963.5, rms=10.849 (9.975%) 033: dt: 0.5000, sse=2932365.0, rms=9.933 (8.445%) 034: dt: 0.5000, sse=2643731.5, rms=9.262 (6.752%) 035: dt: 0.5000, sse=2436878.2, rms=8.749 (5.537%) 036: dt: 0.5000, sse=2283431.8, rms=8.345 (4.624%) 037: dt: 0.5000, sse=2148397.8, rms=7.975 (4.434%) 038: dt: 0.5000, sse=2026504.0, rms=7.625 (4.387%) 039: dt: 0.5000, sse=1907428.2, rms=7.271 (4.640%) 040: dt: 0.5000, sse=1807158.8, rms=6.958 (4.301%) 041: dt: 0.5000, sse=1715035.4, rms=6.661 (4.269%) 042: dt: 0.5000, sse=1648534.1, rms=6.436 (3.377%) 043: dt: 0.5000, sse=1588641.5, rms=6.229 (3.218%) 044: dt: 0.5000, sse=1555030.2, rms=6.107 (1.959%) 045: dt: 0.5000, sse=1521268.1, rms=5.987 (1.972%) 046: dt: 0.5000, sse=1506267.5, rms=5.929 (0.972%) 047: dt: 0.5000, sse=1488130.4, rms=5.862 (1.127%) rms = 5.84, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1482808.5, rms=5.840 (0.380%) 049: dt: 0.2500, sse=1443116.1, rms=5.662 (3.048%) 050: dt: 0.2500, sse=1428818.5, rms=5.605 (1.007%) rms = 5.60, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=1427664.9, rms=5.598 (0.108%) rms = 5.56, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1418147.0, rms=5.558 (0.726%) positioning took 2.4 minutes mean border=52.1, 2070 (19) missing vertices, mean dist 0.2 [0.2 (%54.0)->1.0 (%46.0))] %19 local maxima, %41 large gradients and %34 min vals, 460 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=1567036.8, rms=5.263 053: dt: 0.5000, sse=1506328.2, rms=5.012 (4.781%) 054: dt: 0.5000, sse=1477280.1, rms=4.905 (2.140%) rms = 5.01, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1444698.2, rms=4.731 (3.535%) rms = 4.75, time step reduction 2 of 3 to 0.125... rms = 4.71, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1440784.9, rms=4.709 (0.474%) positioning took 0.7 minutes mean border=51.3, 2285 (10) missing vertices, mean dist 0.2 [0.2 (%49.1)->0.8 (%50.9))] %30 local maxima, %30 large gradients and %33 min vals, 512 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=1521435.2, rms=5.013 rms = 5.09, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1491000.1, rms=4.869 (2.856%) rms = 4.84, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=1486173.2, rms=4.845 (0.504%) rms = 4.82, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1482024.9, rms=4.822 (0.479%) positioning took 0.5 minutes mean border=50.7, 5179 (7) missing vertices, mean dist 0.2 [0.2 (%47.8)->0.6 (%52.2))] %36 local maxima, %23 large gradients and %32 min vals, 546 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-6.0.0/0050566/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1510204.5, rms=4.929 060: dt: 0.5000, sse=1473245.1, rms=4.794 (2.728%) 061: dt: 0.5000, sse=1427920.9, rms=4.629 (3.438%) 062: dt: 0.5000, sse=1413049.4, rms=4.570 (1.285%) 063: dt: 0.5000, sse=1387293.4, rms=4.463 (2.347%) rms = 4.43, time step reduction 1 of 3 to 0.250... 064: dt: 0.5000, sse=1378639.9, rms=4.427 (0.805%) 065: dt: 0.2500, sse=1327745.2, rms=4.121 (6.902%) 066: dt: 0.2500, sse=1307189.4, rms=4.016 (2.542%) rms = 4.05, time step reduction 2 of 3 to 0.125... rms = 3.97, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1299327.6, rms=3.970 (1.163%) positioning took 1.2 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.area.pial vertex spacing 1.10 +- 0.50 (0.08-->8.24) (max @ vno 82855 --> 82845) face area 0.47 +- 0.40 (0.00-->8.33) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 121292 vertices processed 25000 of 121292 vertices processed 50000 of 121292 vertices processed 75000 of 121292 vertices processed 100000 of 121292 vertices processed 0 of 121292 vertices processed 25000 of 121292 vertices processed 50000 of 121292 vertices processed 75000 of 121292 vertices processed 100000 of 121292 vertices processed thickness calculation complete, 781:3388 truncations. 27634 vertices at 0 distance 80520 vertices at 1 distance 72282 vertices at 2 distance 33173 vertices at 3 distance 11185 vertices at 4 distance 3494 vertices at 5 distance 1187 vertices at 6 distance 458 vertices at 7 distance 204 vertices at 8 distance 137 vertices at 9 distance 78 vertices at 10 distance 54 vertices at 11 distance 48 vertices at 12 distance 42 vertices at 13 distance 28 vertices at 14 distance 26 vertices at 15 distance 24 vertices at 16 distance 11 vertices at 17 distance 13 vertices at 18 distance 8 vertices at 19 distance 10 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.thickness positioning took 13.2 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050566 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-6.0.0/0050566/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... 12664 bright wm thresholded. 2174 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.orig... computing class statistics... border white: 240984 voxels (1.44%) border gray 284361 voxels (1.69%) WM (95.0): 96.0 +- 8.6 [70.0 --> 110.0] GM (70.0) : 69.4 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 53.4 (was 70) setting MAX_BORDER_WHITE to 109.6 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 42.9 (was 40) setting MAX_GRAY to 92.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-7.0, GM=64+-8.7 mean inside = 91.7, mean outside = 73.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.91 +- 0.25 (0.03-->3.58) (max @ vno 124624 --> 124652) face area 0.35 +- 0.16 (0.00-->2.58) mean absolute distance = 0.45 +- 0.70 3242 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 32 points - only 0.00% unknown deleting segment 3 with 189 points - only 0.00% unknown deleting segment 4 with 52 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown mean border=77.0, 110 (100) missing vertices, mean dist 0.3 [0.5 (%17.7)->0.5 (%82.3))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.26 (0.11-->4.03) (max @ vno 124624 --> 124652) face area 0.35 +- 0.16 (0.00-->2.60) mean absolute distance = 0.29 +- 0.51 2758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1717081.2, rms=6.759 001: dt: 0.5000, sse=1013887.4, rms=4.038 (40.259%) 002: dt: 0.5000, sse=862353.4, rms=3.173 (21.424%) 003: dt: 0.5000, sse=848221.7, rms=3.087 (2.716%) 004: dt: 0.5000, sse=834038.0, rms=2.931 (5.045%) rms = 3.04, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=726701.8, rms=2.039 (30.428%) 006: dt: 0.2500, sse=690992.4, rms=1.618 (20.631%) 007: dt: 0.2500, sse=682703.8, rms=1.496 (7.537%) rms = 1.45, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=679845.2, rms=1.454 (2.872%) rms = 1.40, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=677341.2, rms=1.405 (3.354%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 29 points - only 0.00% unknown deleting segment 1 with 118 points - only 0.00% unknown deleting segment 2 with 42 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown mean border=79.5, 46 (12) missing vertices, mean dist -0.2 [0.3 (%70.9)->0.2 (%29.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.25 (0.11-->3.82) (max @ vno 124624 --> 124652) face area 0.37 +- 0.17 (0.00-->2.95) mean absolute distance = 0.26 +- 0.41 2973 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1008036.4, rms=3.784 010: dt: 0.5000, sse=806037.6, rms=2.418 (36.110%) rms = 2.58, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=738050.2, rms=1.756 (27.362%) 012: dt: 0.2500, sse=708878.9, rms=1.356 (22.770%) 013: dt: 0.2500, sse=699353.2, rms=1.215 (10.395%) rms = 1.17, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=698006.9, rms=1.174 (3.441%) rms = 1.14, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=695374.9, rms=1.141 (2.757%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 30 points - only 0.00% unknown deleting segment 1 with 120 points - only 0.00% unknown deleting segment 2 with 43 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown mean border=81.2, 48 (8) missing vertices, mean dist -0.1 [0.3 (%64.6)->0.2 (%35.4))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.92 +- 0.25 (0.06-->3.74) (max @ vno 124624 --> 124652) face area 0.36 +- 0.17 (0.00-->2.91) mean absolute distance = 0.25 +- 0.36 2733 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=807220.2, rms=2.581 016: dt: 0.5000, sse=770339.3, rms=2.263 (12.327%) rms = 2.49, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=704492.2, rms=1.537 (32.096%) 018: dt: 0.2500, sse=681535.8, rms=1.189 (22.651%) 019: dt: 0.2500, sse=675996.5, rms=1.091 (8.202%) rms = 1.08, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=683215.8, rms=1.075 (1.467%) rms = 1.04, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=672889.8, rms=1.040 (3.274%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 27 points - only 0.00% unknown deleting segment 1 with 121 points - only 0.00% unknown deleting segment 2 with 47 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown mean border=81.9, 51 (4) missing vertices, mean dist -0.0 [0.3 (%55.1)->0.2 (%44.9))] %86 local maxima, % 9 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-6.0.0/0050566/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=690469.6, rms=1.473 rms = 1.47, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=696567.0, rms=1.466 (0.464%) 023: dt: 0.2500, sse=663522.4, rms=1.024 (30.132%) 024: dt: 0.2500, sse=662714.9, rms=0.892 (12.870%) rms = 0.93, time step reduction 2 of 3 to 0.125... rms = 0.86, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=661098.9, rms=0.857 (4.005%) positioning took 0.4 minutes generating cortex label... 3 non-cortical segments detected only using segment with 7637 vertices erasing segment 0 (vno[0] = 39048) erasing segment 2 (vno[0] = 91649) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.area vertex spacing 0.91 +- 0.25 (0.03-->3.51) (max @ vno 49445 --> 49452) face area 0.35 +- 0.16 (0.00-->2.89) 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 30 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=52.4, 146 (146) missing vertices, mean dist 1.5 [3.8 (%0.0)->2.8 (%100.0))] % 9 local maxima, %44 large gradients and %42 min vals, 761 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=22358734.0, rms=30.207 001: dt: 0.0500, sse=19784170.0, rms=28.361 (6.110%) 002: dt: 0.0500, sse=17935920.0, rms=26.958 (4.947%) 003: dt: 0.0500, sse=16508529.0, rms=25.822 (4.213%) 004: dt: 0.0500, sse=15344590.0, rms=24.858 (3.736%) 005: dt: 0.0500, sse=14357010.0, rms=24.009 (3.415%) 006: dt: 0.0500, sse=13494368.0, rms=23.242 (3.194%) 007: dt: 0.0500, sse=12726657.0, rms=22.537 (3.031%) 008: dt: 0.0500, sse=12032543.0, rms=21.881 (2.914%) 009: dt: 0.0500, sse=11398805.0, rms=21.263 (2.821%) 010: dt: 0.0500, sse=10815420.0, rms=20.679 (2.749%) positioning took 0.9 minutes mean border=52.2, 103 (76) missing vertices, mean dist 1.3 [3.1 (%0.0)->2.3 (%100.0))] %10 local maxima, %44 large gradients and %41 min vals, 753 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=11538971.0, rms=21.397 011: dt: 0.0500, sse=10994248.0, rms=20.855 (2.531%) 012: dt: 0.0500, sse=10487013.0, rms=20.338 (2.481%) 013: dt: 0.0500, sse=10013911.0, rms=19.843 (2.433%) 014: dt: 0.0500, sse=9572053.0, rms=19.369 (2.387%) 015: dt: 0.0500, sse=9159382.0, rms=18.916 (2.340%) 016: dt: 0.0500, sse=8773994.0, rms=18.483 (2.291%) 017: dt: 0.0500, sse=8413631.0, rms=18.068 (2.244%) 018: dt: 0.0500, sse=8077839.0, rms=17.673 (2.188%) 019: dt: 0.0500, sse=7763779.0, rms=17.295 (2.139%) 020: dt: 0.0500, sse=7471131.0, rms=16.935 (2.081%) positioning took 0.9 minutes mean border=52.0, 146 (63) missing vertices, mean dist 1.1 [0.1 (%0.8)->2.0 (%99.2))] %10 local maxima, %44 large gradients and %41 min vals, 747 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=7567063.0, rms=17.057 021: dt: 0.0500, sse=7286535.0, rms=16.707 (2.051%) 022: dt: 0.0500, sse=7025741.5, rms=16.375 (1.988%) 023: dt: 0.0500, sse=6781530.0, rms=16.057 (1.938%) 024: dt: 0.0500, sse=6554461.0, rms=15.757 (1.874%) 025: dt: 0.0500, sse=6342810.5, rms=15.471 (1.814%) 026: dt: 0.0500, sse=6145838.5, rms=15.200 (1.752%) 027: dt: 0.0500, sse=5961316.0, rms=14.941 (1.700%) 028: dt: 0.0500, sse=5787314.0, rms=14.693 (1.660%) 029: dt: 0.0500, sse=5622573.0, rms=14.455 (1.625%) 030: dt: 0.0500, sse=5466583.5, rms=14.225 (1.591%) positioning took 0.9 minutes mean border=51.9, 188 (54) missing vertices, mean dist 1.0 [0.1 (%12.6)->1.9 (%87.4))] %10 local maxima, %44 large gradients and %41 min vals, 722 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=5549698.5, rms=14.345 031: dt: 0.5000, sse=4481932.5, rms=12.675 (11.639%) 032: dt: 0.5000, sse=3790270.2, rms=11.456 (9.620%) 033: dt: 0.5000, sse=3304117.8, rms=10.514 (8.220%) 034: dt: 0.5000, sse=2970424.8, rms=9.807 (6.724%) 035: dt: 0.5000, sse=2723287.2, rms=9.248 (5.701%) 036: dt: 0.5000, sse=2520815.5, rms=8.761 (5.269%) 037: dt: 0.5000, sse=2337009.0, rms=8.297 (5.290%) 038: dt: 0.5000, sse=2169452.8, rms=7.850 (5.387%) 039: dt: 0.5000, sse=2005191.5, rms=7.391 (5.853%) 040: dt: 0.5000, sse=1866066.4, rms=6.975 (5.622%) 041: dt: 0.5000, sse=1750328.5, rms=6.614 (5.174%) 042: dt: 0.5000, sse=1662337.9, rms=6.322 (4.423%) 043: dt: 0.5000, sse=1597132.6, rms=6.100 (3.504%) 044: dt: 0.5000, sse=1550144.6, rms=5.931 (2.775%) 045: dt: 0.5000, sse=1513595.1, rms=5.800 (2.209%) 046: dt: 0.5000, sse=1486593.9, rms=5.698 (1.758%) 047: dt: 0.5000, sse=1464102.8, rms=5.615 (1.457%) 048: dt: 0.5000, sse=1449521.5, rms=5.558 (1.018%) 049: dt: 0.5000, sse=1435256.4, rms=5.504 (0.961%) rms = 5.47, time step reduction 1 of 3 to 0.250... 050: dt: 0.5000, sse=1427120.8, rms=5.471 (0.606%) 051: dt: 0.2500, sse=1386133.4, rms=5.281 (3.476%) 052: dt: 0.2500, sse=1371881.8, rms=5.223 (1.105%) rms = 5.23, time step reduction 2 of 3 to 0.125... rms = 5.20, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=1367870.2, rms=5.205 (0.342%) positioning took 2.7 minutes mean border=51.4, 2541 (13) missing vertices, mean dist 0.2 [0.2 (%53.7)->0.9 (%46.3))] %19 local maxima, %38 large gradients and %36 min vals, 332 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=1594510.6, rms=5.141 054: dt: 0.5000, sse=1529758.4, rms=4.874 (5.202%) 055: dt: 0.5000, sse=1482305.4, rms=4.686 (3.853%) rms = 4.72, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1442797.2, rms=4.474 (4.516%) rms = 4.43, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1436049.1, rms=4.429 (1.011%) 058: dt: 0.1250, sse=1424321.0, rms=4.366 (1.427%) rms = 4.35, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1420498.5, rms=4.348 (0.414%) positioning took 0.9 minutes mean border=50.8, 3017 (13) missing vertices, mean dist 0.2 [0.2 (%51.0)->0.7 (%49.0))] %28 local maxima, %29 large gradients and %36 min vals, 403 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=1485253.2, rms=4.608 rms = 4.60, time step reduction 1 of 3 to 0.250... 060: dt: 0.5000, sse=1480814.4, rms=4.602 (0.126%) 061: dt: 0.2500, sse=1440656.5, rms=4.411 (4.158%) 062: dt: 0.2500, sse=1425294.9, rms=4.340 (1.605%) rms = 4.32, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1420042.0, rms=4.317 (0.516%) 064: dt: 0.1250, sse=1401261.9, rms=4.220 (2.261%) rms = 4.19, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1394510.6, rms=4.188 (0.746%) positioning took 0.9 minutes mean border=50.2, 5869 (12) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.5 (%51.7))] %34 local maxima, %22 large gradients and %34 min vals, 458 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1428204.1, rms=4.265 rms = 4.24, time step reduction 1 of 3 to 0.250... 066: dt: 0.5000, sse=1418002.8, rms=4.239 (0.616%) 067: dt: 0.2500, sse=1370524.6, rms=3.989 (5.885%) 068: dt: 0.2500, sse=1351386.1, rms=3.897 (2.327%) rms = 3.87, time step reduction 2 of 3 to 0.125... 069: dt: 0.2500, sse=1345021.0, rms=3.866 (0.793%) 070: dt: 0.1250, sse=1323515.2, rms=3.740 (3.244%) rms = 3.71, time step reduction 3 of 3 to 0.062... 071: dt: 0.1250, sse=1316838.8, rms=3.706 (0.910%) positioning took 0.9 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.area.pial vertex spacing 1.09 +- 0.51 (0.07-->9.38) (max @ vno 95512 --> 95531) face area 0.47 +- 0.40 (0.00-->9.67) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 125464 vertices processed 25000 of 125464 vertices processed 50000 of 125464 vertices processed 75000 of 125464 vertices processed 100000 of 125464 vertices processed 125000 of 125464 vertices processed 0 of 125464 vertices processed 25000 of 125464 vertices processed 50000 of 125464 vertices processed 75000 of 125464 vertices processed 100000 of 125464 vertices processed 125000 of 125464 vertices processed thickness calculation complete, 815:4164 truncations. 27925 vertices at 0 distance 82016 vertices at 1 distance 74735 vertices at 2 distance 34727 vertices at 3 distance 12421 vertices at 4 distance 3866 vertices at 5 distance 1324 vertices at 6 distance 504 vertices at 7 distance 228 vertices at 8 distance 197 vertices at 9 distance 136 vertices at 10 distance 82 vertices at 11 distance 72 vertices at 12 distance 54 vertices at 13 distance 46 vertices at 14 distance 41 vertices at 15 distance 48 vertices at 16 distance 20 vertices at 17 distance 16 vertices at 18 distance 18 vertices at 19 distance 14 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.thickness positioning took 14.3 minutes PIDs (24766 24769) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 11:26:47 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label Total face volume 255377 Total vertex volume 251169 (mask=0) #@# 0050566 lh 251169 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 11:26:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label Total face volume 268912 Total vertex volume 264656 (mask=0) #@# 0050566 rh 264656 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 11:26:53 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 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 = 213 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/ribbon.mgz mris_volmask took 10.87 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 11:37:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 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 0050566 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 11:37:46 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 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 0050566 rh pial Waiting for PID 25691 of (25691 25694 25697 25700) to complete... Waiting for PID 25694 of (25691 25694 25697 25700) to complete... Waiting for PID 25697 of (25691 25694 25697 25700) to complete... Waiting for PID 25700 of (25691 25694 25697 25700) 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 0050566 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377 Total vertex volume 251169 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1093 787 1750 2.383 0.440 0.090 0.015 6 0.6 bankssts 718 498 1763 2.936 0.677 0.123 0.016 10 0.4 caudalanteriorcingulate 3552 2395 7403 2.640 0.708 0.106 0.017 28 2.4 caudalmiddlefrontal 1786 1354 3073 2.152 0.600 0.156 0.037 24 3.0 cuneus 545 384 2177 3.842 0.867 0.112 0.025 4 0.6 entorhinal 3405 2556 9505 2.929 0.775 0.139 0.029 44 4.2 fusiform 7136 5013 15225 2.511 0.683 0.126 0.028 95 8.5 inferiorparietal 4288 3111 10408 2.584 0.774 0.141 0.041 73 7.9 inferiortemporal 1465 972 3043 2.656 0.862 0.121 0.029 16 1.7 isthmuscingulate 7428 5174 12923 2.195 0.649 0.138 0.032 93 9.6 lateraloccipital 3413 2464 8884 2.940 0.864 0.129 0.028 37 4.0 lateralorbitofrontal 4425 3258 8241 2.267 0.722 0.142 0.035 55 6.6 lingual 2186 1567 5101 2.772 0.729 0.133 0.030 30 2.7 medialorbitofrontal 3822 2785 9426 2.545 0.752 0.127 0.028 49 4.7 middletemporal 839 583 2189 3.185 0.821 0.102 0.023 6 0.6 parahippocampal 2005 1408 3796 2.495 0.657 0.121 0.023 18 1.8 paracentral 2115 1512 4613 2.493 0.707 0.115 0.022 25 2.1 parsopercularis 953 686 2960 3.081 0.861 0.129 0.026 12 1.0 parsorbitalis 1681 1188 3849 2.601 0.672 0.131 0.032 20 2.1 parstriangularis 1866 1457 2449 1.756 0.595 0.155 0.040 23 3.3 pericalcarine 5372 3752 10486 2.221 0.788 0.110 0.021 45 4.7 postcentral 1559 1100 3522 2.674 0.855 0.129 0.026 17 1.7 posteriorcingulate 6316 4458 13317 2.544 0.643 0.116 0.021 57 5.4 precentral 4962 3508 12135 2.794 0.762 0.130 0.031 57 6.4 precuneus 925 590 2579 3.211 0.949 0.111 0.032 10 1.1 rostralanteriorcingulate 8412 5951 17989 2.405 0.730 0.133 0.033 120 12.2 rostralmiddlefrontal 10419 7517 24866 2.824 0.741 0.125 0.027 107 11.7 superiorfrontal 8117 5883 17585 2.464 0.748 0.130 0.026 89 8.9 superiorparietal 4272 3017 9278 2.470 0.778 0.099 0.021 40 3.9 superiortemporal 4115 2958 8445 2.367 0.678 0.141 0.033 55 5.9 supramarginal 330 248 1404 3.050 0.875 0.144 0.049 7 0.6 frontalpole 569 462 3590 4.501 0.550 0.160 0.049 7 1.2 temporalpole 546 376 786 2.030 0.378 0.149 0.024 7 0.5 transversetemporal 2831 1932 6401 3.143 0.847 0.120 0.032 25 3.6 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 0050566 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377 Total vertex volume 251169 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1093 697 1750 2.383 0.440 0.113 0.029 27 1.3 bankssts 718 700 1763 2.936 0.677 0.166 0.035 12 1.2 caudalanteriorcingulate 3552 3184 7403 2.640 0.708 0.152 0.034 39 5.9 caudalmiddlefrontal 1786 1601 3073 2.152 0.600 0.155 0.038 22 3.2 cuneus 545 766 2177 3.842 0.867 0.209 0.044 6 1.2 entorhinal 3405 3685 9505 2.929 0.775 0.190 0.043 47 7.5 fusiform 7136 6984 15225 2.511 0.683 0.173 0.038 96 13.2 inferiorparietal 4288 4779 10408 2.584 0.774 0.208 0.050 77 10.5 inferiortemporal 1465 1312 3043 2.656 0.862 0.175 0.046 29 2.9 isthmuscingulate 7428 6526 12923 2.195 0.649 0.148 0.034 98 12.0 lateraloccipital 3413 3461 8884 2.940 0.864 0.190 0.045 59 8.0 lateralorbitofrontal 4425 4054 8241 2.267 0.722 0.172 0.043 73 9.2 lingual 2186 2120 5101 2.772 0.729 0.186 0.049 36 5.1 medialorbitofrontal 3822 4265 9426 2.545 0.752 0.202 0.043 51 8.4 middletemporal 839 784 2189 3.185 0.821 0.173 0.048 11 1.9 parahippocampal 2005 1649 3796 2.495 0.657 0.138 0.030 26 2.6 paracentral 2115 2218 4613 2.493 0.707 0.177 0.040 26 4.2 parsopercularis 953 1177 2960 3.081 0.861 0.197 0.038 11 1.7 parsorbitalis 1681 1720 3849 2.601 0.672 0.203 0.044 28 3.2 parstriangularis 1866 1361 2449 1.756 0.595 0.145 0.044 30 3.3 pericalcarine 5372 5497 10486 2.221 0.788 0.169 0.036 57 10.2 postcentral 1559 1388 3522 2.674 0.855 0.166 0.049 65 3.1 posteriorcingulate 6316 5667 13317 2.544 0.643 0.144 0.030 83 9.0 precentral 4962 4855 12135 2.794 0.762 0.187 0.048 93 11.1 precuneus 925 907 2579 3.211 0.949 0.188 0.052 17 2.1 rostralanteriorcingulate 8412 8588 17989 2.405 0.730 0.188 0.041 112 18.2 rostralmiddlefrontal 10419 9903 24866 2.824 0.741 0.166 0.039 153 19.1 superiorfrontal 8117 7933 17585 2.464 0.748 0.167 0.038 103 15.1 superiorparietal 4272 4220 9278 2.470 0.778 0.170 0.036 58 8.0 superiortemporal 4115 4022 8445 2.367 0.678 0.181 0.039 53 7.9 supramarginal 330 629 1404 3.050 0.875 0.306 0.051 5 1.0 frontalpole 569 1042 3590 4.501 0.550 0.239 0.039 4 1.2 temporalpole 546 420 786 2.030 0.378 0.147 0.037 6 0.9 transversetemporal 2831 2091 6401 3.143 0.847 0.171 0.050 55 6.7 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 0050566 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912 Total vertex volume 264656 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1285 919 2410 2.583 0.587 0.101 0.014 8 0.8 bankssts 1270 899 2612 2.711 0.707 0.138 0.016 20 0.9 caudalanteriorcingulate 3152 2178 7387 2.831 0.732 0.109 0.019 24 2.5 caudalmiddlefrontal 2321 1699 3830 2.063 0.575 0.149 0.034 30 3.3 cuneus 583 407 2167 3.609 0.828 0.114 0.024 4 0.6 entorhinal 3782 2688 9770 2.896 0.828 0.136 0.032 48 4.8 fusiform 7491 5294 17345 2.639 0.709 0.128 0.030 93 9.4 inferiorparietal 3424 2515 9444 2.760 0.829 0.140 0.034 53 5.2 inferiortemporal 1144 771 2468 2.665 0.871 0.123 0.030 15 1.0 isthmuscingulate 7558 5106 12776 2.212 0.716 0.135 0.032 98 9.7 lateraloccipital 2866 2077 8866 3.250 0.926 0.136 0.038 38 4.4 lateralorbitofrontal 4625 3426 8878 2.284 0.706 0.152 0.039 64 8.4 lingual 2448 1774 6212 2.725 0.826 0.142 0.041 45 4.2 medialorbitofrontal 4073 3014 11286 2.773 0.879 0.139 0.032 67 5.8 middletemporal 911 610 2138 2.812 0.957 0.093 0.019 7 0.5 parahippocampal 2271 1585 4517 2.574 0.582 0.129 0.029 22 2.8 paracentral 2081 1494 5019 2.699 0.703 0.124 0.022 25 1.9 parsopercularis 1032 754 3823 3.452 0.942 0.141 0.030 14 1.3 parsorbitalis 2195 1542 5226 2.564 0.766 0.118 0.022 23 2.0 parstriangularis 2413 1702 2442 1.658 0.394 0.137 0.033 27 3.4 pericalcarine 5534 3653 9641 2.123 0.810 0.101 0.022 57 5.3 postcentral 1715 1240 3759 2.692 0.813 0.144 0.030 24 2.2 posteriorcingulate 6303 4251 12092 2.453 0.793 0.110 0.023 65 6.5 precentral 5510 3844 12152 2.702 0.809 0.129 0.025 60 6.0 precuneus 742 472 1768 3.014 0.892 0.142 0.036 11 1.2 rostralanteriorcingulate 7581 5391 18158 2.635 0.765 0.136 0.033 102 10.7 rostralmiddlefrontal 10097 7057 25797 2.890 0.749 0.124 0.027 107 10.7 superiorfrontal 8561 5895 17554 2.473 0.764 0.115 0.023 71 8.1 superiorparietal 4835 3483 11835 2.612 0.938 0.098 0.017 40 3.8 superiortemporal 4725 3285 11204 2.591 0.824 0.129 0.026 59 5.3 supramarginal 473 348 1792 2.965 0.787 0.195 0.058 11 1.3 frontalpole 641 517 2566 3.522 0.970 0.158 0.030 10 1.1 temporalpole 573 390 848 1.939 0.428 0.145 0.026 10 0.6 transversetemporal 3028 2068 6855 3.087 0.882 0.122 0.028 30 3.4 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 0050566 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912 Total vertex volume 264656 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1285 911 2410 2.583 0.587 0.141 0.030 16 1.8 bankssts 1270 1002 2612 2.711 0.707 0.145 0.032 28 1.7 caudalanteriorcingulate 3152 2906 7387 2.831 0.732 0.144 0.030 36 4.6 caudalmiddlefrontal 2321 2165 3830 2.063 0.575 0.154 0.035 33 3.8 cuneus 583 804 2167 3.609 0.828 0.206 0.044 8 1.3 entorhinal 3782 3756 9770 2.896 0.828 0.162 0.037 60 6.3 fusiform 7491 7489 17345 2.639 0.709 0.170 0.034 98 12.8 inferiorparietal 3424 3947 9444 2.760 0.829 0.207 0.048 60 8.2 inferiortemporal 1144 1047 2468 2.665 0.871 0.170 0.047 47 2.3 isthmuscingulate 7558 6416 12776 2.212 0.716 0.136 0.033 115 11.2 lateraloccipital 2866 3051 8866 3.250 0.926 0.205 0.052 64 7.2 lateralorbitofrontal 4625 4422 8878 2.284 0.706 0.174 0.041 71 9.5 lingual 2448 2740 6212 2.725 0.826 0.211 0.052 41 6.2 medialorbitofrontal 4073 4839 11286 2.773 0.879 0.199 0.038 102 7.7 middletemporal 911 845 2138 2.812 0.957 0.168 0.044 12 1.9 parahippocampal 2271 1888 4517 2.574 0.582 0.143 0.035 27 3.6 paracentral 2081 2099 5019 2.699 0.703 0.173 0.033 28 3.3 parsopercularis 1032 1406 3823 3.452 0.942 0.211 0.043 17 2.1 parsorbitalis 2195 2406 5226 2.564 0.766 0.191 0.037 29 4.0 parstriangularis 2413 1437 2442 1.658 0.394 0.114 0.031 34 3.5 pericalcarine 5534 5003 9641 2.123 0.810 0.138 0.029 56 8.0 postcentral 1715 1531 3759 2.692 0.813 0.171 0.049 49 3.9 posteriorcingulate 6303 5390 12092 2.453 0.793 0.133 0.026 75 8.0 precentral 5510 4897 12152 2.702 0.809 0.165 0.042 85 10.5 precuneus 742 681 1768 3.014 0.892 0.179 0.048 13 1.7 rostralanteriorcingulate 7581 7830 18158 2.635 0.765 0.187 0.043 108 16.3 rostralmiddlefrontal 10097 10227 25797 2.890 0.749 0.174 0.040 133 19.4 superiorfrontal 8561 7760 17554 2.473 0.764 0.145 0.030 97 12.6 superiorparietal 4835 5063 11835 2.612 0.938 0.166 0.033 58 8.0 superiortemporal 4725 4806 11204 2.591 0.824 0.175 0.039 60 9.1 supramarginal 473 862 1792 2.965 0.787 0.313 0.066 9 1.7 frontalpole 641 982 2566 3.522 0.970 0.229 0.047 7 1.5 temporalpole 573 486 848 1.939 0.428 0.151 0.039 7 1.0 transversetemporal 3028 2120 6855 3.087 0.882 0.161 0.053 60 7.8 insula PIDs (25691 25694 25697 25700) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 11:38:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 11:38:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 25803 of (25803 25806) to complete... Waiting for PID 25806 of (25803 25806) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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... 42 labels changed using aseg relabeling using gibbs priors... 000: 7819 changed, 121292 examined... 001: 1734 changed, 30607 examined... 002: 494 changed, 9321 examined... 003: 210 changed, 2846 examined... 004: 104 changed, 1222 examined... 005: 58 changed, 625 examined... 006: 28 changed, 325 examined... 007: 12 changed, 163 examined... 008: 7 changed, 81 examined... 009: 2 changed, 38 examined... 010: 1 changed, 14 examined... 011: 0 changed, 7 examined... 18 labels changed using aseg 000: 233 total segments, 149 labels (1720 vertices) changed 001: 90 total segments, 7 labels (27 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 728 vertices marked for relabeling... 728 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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... 66 labels changed using aseg relabeling using gibbs priors... 000: 7972 changed, 125464 examined... 001: 1746 changed, 31120 examined... 002: 503 changed, 9260 examined... 003: 203 changed, 2863 examined... 004: 95 changed, 1154 examined... 005: 43 changed, 541 examined... 006: 28 changed, 227 examined... 007: 14 changed, 159 examined... 008: 9 changed, 80 examined... 009: 5 changed, 45 examined... 010: 5 changed, 31 examined... 011: 2 changed, 24 examined... 012: 0 changed, 8 examined... 42 labels changed using aseg 000: 210 total segments, 126 labels (1848 vertices) changed 001: 92 total segments, 9 labels (67 vertices) changed 002: 84 total segments, 1 labels (1 vertices) changed 003: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 809 vertices marked for relabeling... 809 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. PIDs (25803 25806) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 11:39:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 11:39:15 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh white Waiting for PID 25852 of (25852 25855) to complete... Waiting for PID 25855 of (25852 25855) 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 0050566 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377 Total vertex volume 251169 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1118 801 2667 2.406 1.062 0.142 0.040 16 1.9 G&S_frontomargin 1267 963 2822 2.392 0.710 0.147 0.031 17 1.6 G&S_occipital_inf 1701 1183 3421 2.318 0.577 0.133 0.028 17 2.1 G&S_paracentral 1183 866 3246 2.665 0.751 0.138 0.033 16 1.4 G&S_subcentral 559 397 1802 2.805 0.780 0.137 0.049 13 1.0 G&S_transv_frontopol 1934 1335 4554 2.968 0.795 0.107 0.022 13 1.6 G&S_cingul-Ant 1028 722 2323 2.784 0.680 0.102 0.017 7 0.7 G&S_cingul-Mid-Ant 1246 887 2694 2.822 0.730 0.118 0.025 9 1.3 G&S_cingul-Mid-Post 464 334 1595 3.209 0.704 0.157 0.040 6 0.7 G_cingul-Post-dorsal 271 184 754 2.983 0.890 0.144 0.044 4 0.4 G_cingul-Post-ventral 1760 1371 3319 2.133 0.607 0.173 0.044 29 3.6 G_cuneus 1204 843 3277 2.696 0.798 0.126 0.029 20 1.5 G_front_inf-Opercular 340 234 1227 3.478 0.442 0.151 0.038 6 0.6 G_front_inf-Orbital 904 642 2513 2.682 0.598 0.150 0.045 16 1.6 G_front_inf-Triangul 4647 3265 12934 2.754 0.784 0.146 0.038 86 7.8 G_front_middle 7202 5146 19785 3.019 0.722 0.139 0.033 94 10.0 G_front_sup 569 376 1505 3.402 0.834 0.134 0.044 8 1.0 G_Ins_lg&S_cent_ins 647 446 2290 3.536 0.813 0.129 0.040 7 1.0 G_insular_short 2339 1564 5857 2.726 0.694 0.143 0.033 36 3.2 G_occipital_middle 1548 1144 2815 2.062 0.500 0.140 0.024 20 1.5 G_occipital_sup 1302 957 4467 3.246 0.657 0.146 0.029 22 1.5 G_oc-temp_lat-fusifor 2936 2115 5731 2.266 0.726 0.154 0.041 43 5.3 G_oc-temp_med-Lingual 1005 691 3383 3.546 0.795 0.104 0.024 6 0.8 G_oc-temp_med-Parahip 2304 1699 7346 3.049 0.795 0.143 0.036 34 3.3 G_orbital 2735 1942 7024 2.557 0.797 0.156 0.044 51 5.5 G_pariet_inf-Angular 2075 1494 5244 2.548 0.719 0.159 0.039 39 3.7 G_pariet_inf-Supramar 2908 2224 8692 2.790 0.810 0.153 0.035 44 4.4 G_parietal_sup 2102 1473 4897 2.403 0.821 0.129 0.026 23 2.2 G_postcentral 2121 1545 5777 2.765 0.661 0.134 0.028 26 2.4 G_precentral 2425 1745 8681 3.207 0.746 0.155 0.042 40 4.3 G_precuneus 767 610 2345 2.752 0.652 0.181 0.045 17 1.5 G_rectus 402 239 728 2.748 0.778 0.077 0.028 3 0.3 G_subcallosal 334 230 614 2.223 0.549 0.139 0.026 4 0.3 G_temp_sup-G_T_transv 1526 1149 5166 2.787 0.898 0.155 0.038 30 2.9 G_temp_sup-Lateral 667 454 1925 3.413 1.001 0.089 0.026 8 0.5 G_temp_sup-Plan_polar 512 364 767 1.933 0.414 0.048 0.013 1 0.1 G_temp_sup-Plan_tempo 2522 1875 6839 2.552 0.753 0.171 0.059 64 7.0 G_temporal_inf 2023 1516 6193 2.683 0.733 0.155 0.041 43 3.7 G_temporal_middle 263 187 530 2.646 0.835 0.107 0.016 2 0.1 Lat_Fis-ant-Horizont 226 170 404 2.481 0.647 0.106 0.015 1 0.1 Lat_Fis-ant-Vertical 819 555 997 2.095 0.511 0.108 0.017 5 0.6 Lat_Fis-post 2099 1455 2968 1.856 0.509 0.151 0.040 33 3.4 Pole_occipital 1426 1099 6939 3.756 0.945 0.157 0.045 22 2.6 Pole_temporal 2428 1869 3187 1.930 0.761 0.139 0.036 26 3.7 S_calcarine 2668 1869 3338 1.946 0.604 0.095 0.014 14 1.4 S_central 1083 745 1638 2.254 0.576 0.089 0.011 5 0.5 S_cingul-Marginalis 527 385 1026 3.048 0.694 0.089 0.015 2 0.3 S_circular_insula_ant 1217 820 1916 2.635 0.770 0.091 0.012 5 0.6 S_circular_insula_inf 1398 972 2262 2.709 0.559 0.101 0.017 6 1.0 S_circular_insula_sup 829 627 1618 2.601 0.535 0.117 0.019 6 0.7 S_collat_transv_ant 451 302 565 2.153 0.385 0.111 0.018 3 0.4 S_collat_transv_post 2544 1748 3891 2.218 0.512 0.107 0.020 17 2.1 S_front_inf 1545 1076 2100 2.173 0.491 0.101 0.019 8 1.1 S_front_middle 2856 2146 5162 2.321 0.541 0.103 0.016 21 1.9 S_front_sup 191 147 240 1.799 0.305 0.140 0.043 2 0.2 S_interm_prim-Jensen 2509 1752 3706 2.234 0.559 0.109 0.017 19 1.8 S_intrapariet&P_trans 1105 755 1314 2.024 0.415 0.123 0.027 8 1.1 S_oc_middle&Lunatus 1594 1077 2109 2.170 0.626 0.112 0.021 12 1.3 S_oc_sup&transversal 787 534 1127 2.235 0.563 0.083 0.012 3 0.4 S_occipital_ant 692 497 1201 2.524 0.813 0.127 0.029 8 0.7 S_oc-temp_lat 1906 1420 3669 2.634 0.633 0.122 0.024 14 1.9 S_oc-temp_med&Lingual 337 235 461 1.997 0.424 0.096 0.012 1 0.2 S_orbital_lateral 456 357 1028 3.072 0.975 0.118 0.024 4 0.4 S_orbital_med-olfact 1304 880 2772 2.748 0.981 0.112 0.019 10 1.0 S_orbital-H_Shaped 1738 1248 3080 2.529 0.676 0.101 0.016 11 1.0 S_parieto_occipital 1121 694 1101 2.070 0.618 0.117 0.021 18 1.0 S_pericallosal 2881 1962 4515 2.396 0.553 0.094 0.017 16 1.9 S_postcentral 1682 1158 2806 2.383 0.615 0.101 0.014 11 1.0 S_precentral-inf-part 1384 980 2169 2.415 0.529 0.091 0.011 6 0.6 S_precentral-sup-part 617 406 1151 2.780 0.756 0.115 0.020 6 0.5 S_suborbital 1100 727 1647 2.351 0.575 0.113 0.023 7 1.1 S_subparietal 1449 1009 2031 2.135 0.644 0.106 0.016 8 1.0 S_temporal_inf 5380 3815 8963 2.377 0.520 0.095 0.015 34 3.3 S_temporal_sup 227 181 317 1.897 0.311 0.100 0.007 1 0.1 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 0050566 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912 Total vertex volume 264656 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 808 600 1966 2.362 0.695 0.174 0.052 16 1.9 G&S_frontomargin 1157 832 2597 2.707 0.674 0.133 0.027 14 1.3 G&S_occipital_inf 1606 1047 2762 2.226 0.637 0.142 0.042 28 3.2 G&S_paracentral 997 729 3073 2.837 0.941 0.129 0.028 11 1.0 G&S_subcentral 1089 801 3378 2.833 0.821 0.159 0.032 18 1.5 G&S_transv_frontopol 2921 2046 6635 2.759 0.770 0.131 0.030 40 3.4 G&S_cingul-Ant 1731 1212 3766 2.826 0.629 0.128 0.022 19 1.5 G&S_cingul-Mid-Ant 1648 1188 3597 2.728 0.756 0.133 0.028 18 2.1 G&S_cingul-Mid-Post 399 313 1236 2.832 0.575 0.169 0.050 6 0.8 G_cingul-Post-dorsal 300 190 1024 3.398 1.101 0.140 0.036 5 0.4 G_cingul-Post-ventral 2299 1697 3852 1.954 0.580 0.151 0.034 31 3.2 G_cuneus 1240 904 3878 2.957 0.826 0.155 0.038 24 2.1 G_front_inf-Opercular 362 245 1172 3.045 0.700 0.125 0.023 4 0.4 G_front_inf-Orbital 1001 720 3207 2.908 0.719 0.145 0.031 17 1.4 G_front_inf-Triangul 3847 2689 12438 3.038 0.822 0.152 0.040 68 6.7 G_front_middle 5864 4080 18161 3.146 0.693 0.135 0.031 77 7.2 G_front_sup 507 357 1227 2.862 0.941 0.135 0.033 8 0.6 G_Ins_lg&S_cent_ins 852 555 2453 3.291 1.073 0.123 0.044 11 1.4 G_insular_short 2216 1551 6149 2.756 0.713 0.169 0.045 44 4.2 G_occipital_middle 1530 1026 2965 2.335 0.627 0.129 0.033 18 2.1 G_occipital_sup 1878 1382 5327 2.877 0.760 0.161 0.043 31 3.7 G_oc-temp_lat-fusifor 3102 2322 6838 2.378 0.713 0.170 0.047 52 6.7 G_oc-temp_med-Lingual 950 634 3094 3.400 0.886 0.108 0.024 8 0.7 G_oc-temp_med-Parahip 2179 1625 8822 3.522 0.913 0.161 0.045 39 4.3 G_orbital 2904 2147 9241 2.911 0.824 0.157 0.040 57 5.0 G_pariet_inf-Angular 2287 1611 6995 2.829 0.942 0.148 0.036 38 3.7 G_pariet_inf-Supramar 2881 2065 8133 2.729 0.881 0.136 0.033 32 3.9 G_parietal_sup 2030 1320 4078 2.228 0.777 0.123 0.030 26 2.7 G_postcentral 2521 1674 6098 2.684 0.847 0.123 0.029 40 3.3 G_precentral 2255 1683 6833 2.999 0.836 0.147 0.032 32 3.3 G_precuneus 796 626 2778 2.841 0.879 0.189 0.067 19 2.5 G_rectus 149 85 342 2.901 1.206 0.123 0.088 4 0.5 G_subcallosal 420 298 844 2.112 0.535 0.136 0.025 8 0.4 G_temp_sup-G_T_transv 1524 1191 5707 3.040 0.863 0.154 0.030 28 2.3 G_temp_sup-Lateral 775 560 2186 3.407 0.993 0.082 0.016 3 0.5 G_temp_sup-Plan_polar 670 483 1377 2.456 0.573 0.057 0.006 1 0.2 G_temp_sup-Plan_tempo 1745 1295 6203 2.953 0.834 0.152 0.042 34 3.5 G_temporal_inf 2166 1655 7597 2.978 0.862 0.167 0.048 53 4.6 G_temporal_middle 380 261 474 2.036 0.541 0.079 0.009 1 0.1 Lat_Fis-ant-Horizont 309 222 482 2.228 0.566 0.082 0.011 1 0.1 Lat_Fis-ant-Vertical 1156 793 1657 2.460 0.589 0.112 0.020 9 0.9 Lat_Fis-post 3953 2641 5150 1.806 0.598 0.142 0.038 56 6.3 Pole_occipital 1720 1313 6930 3.591 0.952 0.146 0.027 29 2.3 Pole_temporal 2327 1621 2894 2.063 0.821 0.114 0.024 17 2.3 S_calcarine 2510 1644 2502 1.720 0.520 0.076 0.010 10 1.0 S_central 1358 943 2387 2.570 0.626 0.122 0.021 12 1.2 S_cingul-Marginalis 464 320 1021 3.327 0.812 0.079 0.013 1 0.2 S_circular_insula_ant 1079 731 1571 2.384 0.835 0.084 0.010 4 0.4 S_circular_insula_inf 1361 934 2302 2.851 0.605 0.105 0.016 7 1.0 S_circular_insula_sup 714 499 1242 2.392 0.609 0.099 0.015 4 0.3 S_collat_transv_ant 384 268 405 1.930 0.381 0.124 0.027 3 0.4 S_collat_transv_post 2035 1374 3263 2.471 0.578 0.097 0.015 12 1.3 S_front_inf 2002 1437 3652 2.480 0.594 0.105 0.020 12 1.4 S_front_middle 2664 1909 4726 2.537 0.537 0.097 0.017 15 1.8 S_front_sup 241 161 276 1.792 0.478 0.108 0.014 2 0.2 S_interm_prim-Jensen 3682 2467 5736 2.295 0.645 0.092 0.013 22 1.8 S_intrapariet&P_trans 997 669 1200 1.954 0.418 0.113 0.020 7 0.9 S_oc_middle&Lunatus 1428 962 2034 2.348 0.488 0.100 0.016 9 0.9 S_oc_sup&transversal 624 458 876 2.361 0.572 0.128 0.026 5 0.7 S_occipital_ant 737 530 1686 2.801 0.819 0.143 0.039 9 1.0 S_oc-temp_lat 1997 1393 3303 2.516 0.595 0.104 0.015 13 1.2 S_oc-temp_med&Lingual 358 245 460 2.067 0.413 0.114 0.021 2 0.3 S_orbital_lateral 476 341 1441 3.595 0.961 0.103 0.032 5 0.5 S_orbital_med-olfact 1023 739 2391 2.804 0.951 0.139 0.030 11 1.4 S_orbital-H_Shaped 2096 1438 3144 2.378 0.626 0.117 0.019 16 1.6 S_parieto_occipital 1300 822 1258 2.047 0.588 0.120 0.017 23 0.8 S_pericallosal 2712 1781 3546 2.250 0.503 0.085 0.014 11 1.5 S_postcentral 1584 1084 2353 2.189 0.616 0.093 0.012 9 0.8 S_precentral-inf-part 1250 876 2298 2.734 0.564 0.098 0.014 7 0.7 S_precentral-sup-part 362 247 481 2.254 0.597 0.080 0.009 2 0.1 S_suborbital 1252 849 2069 2.378 0.545 0.116 0.022 12 1.1 S_subparietal 953 701 1484 2.181 0.563 0.115 0.017 5 0.7 S_temporal_inf 5864 4035 9631 2.436 0.638 0.094 0.015 36 3.5 S_temporal_sup 288 198 301 1.896 0.374 0.142 0.014 4 0.2 S_temporal_transverse PIDs (25852 25855) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 11:39:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 11:39:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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 25919 of (25919 25922) to complete... Waiting for PID 25922 of (25919 25922) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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... 1277 labels changed using aseg relabeling using gibbs priors... 000: 1779 changed, 121292 examined... 001: 411 changed, 8322 examined... 002: 114 changed, 2369 examined... 003: 59 changed, 665 examined... 004: 28 changed, 311 examined... 005: 14 changed, 163 examined... 006: 7 changed, 90 examined... 007: 6 changed, 49 examined... 008: 4 changed, 37 examined... 009: 4 changed, 23 examined... 010: 1 changed, 23 examined... 011: 1 changed, 8 examined... 012: 2 changed, 6 examined... 013: 2 changed, 12 examined... 014: 1 changed, 13 examined... 015: 1 changed, 6 examined... 016: 1 changed, 7 examined... 017: 0 changed, 7 examined... 230 labels changed using aseg 000: 52 total segments, 19 labels (123 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 597 vertices marked for relabeling... 597 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050566 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... 1150 labels changed using aseg relabeling using gibbs priors... 000: 1925 changed, 125464 examined... 001: 427 changed, 8986 examined... 002: 121 changed, 2392 examined... 003: 49 changed, 684 examined... 004: 31 changed, 267 examined... 005: 21 changed, 154 examined... 006: 18 changed, 113 examined... 007: 17 changed, 91 examined... 008: 8 changed, 77 examined... 009: 7 changed, 40 examined... 010: 8 changed, 35 examined... 011: 6 changed, 39 examined... 012: 7 changed, 35 examined... 013: 6 changed, 35 examined... 014: 5 changed, 34 examined... 015: 3 changed, 23 examined... 016: 2 changed, 17 examined... 017: 4 changed, 16 examined... 018: 4 changed, 19 examined... 019: 3 changed, 22 examined... 020: 1 changed, 15 examined... 021: 0 changed, 5 examined... 256 labels changed using aseg 000: 51 total segments, 18 labels (150 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 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... 614 vertices marked for relabeling... 614 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. PIDs (25919 25922) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 11:40:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 11:40:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh white Waiting for PID 25986 of (25986 25989) to complete... Waiting for PID 25989 of (25986 25989) 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 0050566 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 255377 Total vertex volume 251169 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1294 888 2836 2.817 0.664 0.110 0.018 13 0.8 caudalanteriorcingulate 3813 2586 7826 2.609 0.706 0.106 0.017 30 2.6 caudalmiddlefrontal 2500 1856 4388 2.186 0.558 0.146 0.032 31 3.6 cuneus 470 330 1851 3.796 0.804 0.106 0.024 3 0.5 entorhinal 3111 2323 7847 2.835 0.731 0.133 0.026 35 3.3 fusiform 7138 4991 14871 2.481 0.691 0.127 0.029 91 8.7 inferiorparietal 4266 3142 11863 2.713 0.849 0.150 0.045 81 8.6 inferiortemporal 1451 962 3050 2.666 0.859 0.122 0.030 16 1.7 isthmuscingulate 7406 5162 12993 2.203 0.650 0.139 0.032 95 9.6 lateraloccipital 3593 2608 10473 3.069 0.937 0.135 0.035 46 5.2 lateralorbitofrontal 4550 3323 8289 2.246 0.716 0.143 0.035 57 6.8 lingual 1737 1274 4314 2.791 0.701 0.140 0.031 26 2.2 medialorbitofrontal 5235 3797 11814 2.502 0.698 0.119 0.026 63 5.6 middletemporal 878 609 2297 3.198 0.813 0.100 0.022 6 0.6 parahippocampal 2334 1649 4714 2.560 0.650 0.123 0.024 22 2.3 paracentral 1928 1379 4203 2.513 0.698 0.117 0.023 24 1.9 parsopercularis 984 690 2520 2.931 0.787 0.115 0.024 10 1.0 parsorbitalis 2109 1484 4315 2.416 0.636 0.122 0.028 22 2.3 parstriangularis 1870 1458 2400 1.743 0.588 0.156 0.040 24 3.3 pericalcarine 6243 4376 11993 2.218 0.762 0.112 0.021 52 5.4 postcentral 1707 1207 3664 2.644 0.854 0.129 0.026 18 1.9 posteriorcingulate 6222 4380 13136 2.551 0.647 0.115 0.022 55 5.3 precentral 4885 3501 12566 2.832 0.766 0.136 0.033 61 6.8 precuneus 1307 860 3394 3.173 0.894 0.115 0.030 15 1.5 rostralanteriorcingulate 6185 4384 13272 2.398 0.690 0.135 0.033 90 9.0 rostralmiddlefrontal 11499 8271 27778 2.772 0.775 0.127 0.028 128 13.7 superiorfrontal 6378 4613 14010 2.508 0.773 0.124 0.025 64 6.6 superiorparietal 5570 3997 14083 2.689 0.975 0.107 0.025 54 5.9 superiortemporal 3710 2685 7811 2.418 0.676 0.142 0.032 50 5.6 supramarginal 547 378 786 2.017 0.391 0.147 0.023 7 0.5 transversetemporal 2516 1722 5813 3.098 0.771 0.118 0.028 22 2.8 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 0050566 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 268912 Total vertex volume 264656 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1555 1072 3531 2.811 0.760 0.137 0.019 25 1.2 caudalanteriorcingulate 3273 2263 7609 2.826 0.730 0.109 0.019 25 2.5 caudalmiddlefrontal 2827 2033 4766 2.113 0.615 0.145 0.033 34 3.8 cuneus 567 397 1969 3.603 0.827 0.111 0.023 4 0.5 entorhinal 3412 2461 8455 2.785 0.731 0.137 0.033 44 4.5 fusiform 7419 5241 17186 2.650 0.700 0.128 0.029 92 9.3 inferiorparietal 3798 2754 10936 2.876 0.906 0.137 0.033 57 5.5 inferiortemporal 1132 756 2416 2.666 0.861 0.122 0.030 15 0.9 isthmuscingulate 7642 5168 12871 2.200 0.712 0.136 0.032 100 9.8 lateraloccipital 3266 2376 9934 3.101 1.037 0.145 0.044 49 6.0 lateralorbitofrontal 4541 3368 8724 2.284 0.704 0.153 0.040 63 8.3 lingual 1732 1272 4878 2.850 0.877 0.144 0.047 31 3.4 medialorbitofrontal 5077 3723 13091 2.726 0.842 0.132 0.029 74 6.5 middletemporal 939 630 2202 2.804 0.950 0.092 0.019 7 0.6 parahippocampal 2380 1656 4800 2.583 0.584 0.126 0.029 23 2.8 paracentral 2319 1667 5473 2.688 0.697 0.125 0.022 27 2.2 parsopercularis 972 666 3011 3.177 0.849 0.121 0.025 9 1.1 parsorbitalis 2087 1472 4936 2.544 0.757 0.118 0.023 22 1.9 parstriangularis 2387 1683 2440 1.665 0.398 0.135 0.032 26 3.3 pericalcarine 6246 4147 10917 2.140 0.803 0.103 0.022 62 6.0 postcentral 1860 1367 4240 2.689 0.796 0.151 0.034 28 2.9 posteriorcingulate 6064 4040 11481 2.429 0.805 0.109 0.023 63 6.2 precentral 5605 3923 12503 2.715 0.805 0.127 0.025 60 6.0 precuneus 917 597 2178 3.000 0.852 0.138 0.033 12 1.2 rostralanteriorcingulate 5423 3835 13576 2.721 0.791 0.139 0.035 77 8.2 rostralmiddlefrontal 12596 8900 31729 2.828 0.743 0.127 0.027 144 13.7 superiorfrontal 7257 4977 14938 2.480 0.778 0.113 0.023 60 6.8 superiorparietal 6300 4600 16124 2.722 0.953 0.107 0.019 57 5.6 superiortemporal 4435 3095 10660 2.608 0.833 0.129 0.026 55 5.0 supramarginal 562 382 846 1.939 0.436 0.139 0.026 9 0.6 transversetemporal 2656 1823 6236 3.151 0.860 0.118 0.023 24 2.4 insula PIDs (25986 25989) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 11:40:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts pctsurfcon --s 0050566 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 11:40:40 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts pctsurfcon --s 0050566 --rh-only Waiting for PID 26051 of (26051 26063) to complete... Waiting for PID 26063 of (26051 26063) to complete... pctsurfcon --s 0050566 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts/pctsurfcon.log Sun Oct 8 11:40:40 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-6.0.0/0050566/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-604 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-6.0.0/0050566/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.wm.mgh --regheader 0050566 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 70663 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.wm.mgh Dim: 121292 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.gm.mgh --projfrac 0.3 --regheader 0050566 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 82900 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.gm.mgh Dim: 121292 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26051/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.w-g.pct.mgh --annot 0050566 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/lh.w-g.pct.mgh --annot 0050566 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-604 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/lh.w-g.pct.mgh Vertex Area is 0.709777 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 0050566 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/scripts/pctsurfcon.log Sun Oct 8 11:40:40 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-6.0.0/0050566/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-604 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-6.0.0/0050566/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.wm.mgh --regheader 0050566 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 72864 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.wm.mgh Dim: 125464 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.gm.mgh --projfrac 0.3 --regheader 0050566 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 85791 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.gm.mgh Dim: 125464 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/tmp.pctsurfcon.26063/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.w-g.pct.mgh --annot 0050566 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.w-g.pct.mgh --annot 0050566 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-604 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.w-g.pct.mgh Vertex Area is 0.699236 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 (26051 26063) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 11:40:45 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1954 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1631 voxels changed to hypointensity... 3698 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 11:41:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 mri_aparc2aseg --s 0050566 --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 11:41:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 mri_aparc2aseg --s 0050566 --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 11:41:06 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 mri_aparc2aseg --s 0050566 --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 26219 of (26219 26222 26225) to complete... Waiting for PID 26222 of (26219 26222 26225) to complete... Waiting for PID 26225 of (26219 26222 26225) to complete... mri_aparc2aseg --s 0050566 --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 0050566 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-6.0.0/0050566/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.36 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 12 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 95 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 90 rescaling Left_Hippocampus from 57 --> 60 rescaling Left_Amygdala from 56 --> 59 rescaling CSF from 32 --> 27 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 93 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 55 rescaling Right_Lateral_Ventricle from 13 --> 10 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 55 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 71 rescaling Right_Pallidum from 97 --> 87 rescaling Right_Hippocampus from 53 --> 59 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 24 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512199 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 127 changed. pass 2: 8 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050566 --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 0050566 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-6.0.0/0050566/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.36 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 12 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 95 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 90 rescaling Left_Hippocampus from 57 --> 60 rescaling Left_Amygdala from 56 --> 59 rescaling CSF from 32 --> 27 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 93 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 55 rescaling Right_Lateral_Ventricle from 13 --> 10 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 55 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 71 rescaling Right_Pallidum from 97 --> 87 rescaling Right_Hippocampus from 53 --> 59 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 24 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512138 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 127 changed. pass 2: 8 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050566 --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 0050566 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/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-6.0.0/0050566/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.36 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 54 rescaling Left_Lateral_Ventricle from 13 --> 12 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 55 rescaling Left_Thalamus from 94 --> 95 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 69 rescaling Left_Putamen from 80 --> 78 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 90 rescaling Left_Hippocampus from 57 --> 60 rescaling Left_Amygdala from 56 --> 59 rescaling CSF from 32 --> 27 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 93 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 55 rescaling Right_Lateral_Ventricle from 13 --> 10 rescaling Right_Inf_Lat_Vent from 25 --> 25 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 55 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 71 rescaling Right_Pallidum from 97 --> 87 rescaling Right_Hippocampus from 53 --> 59 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 24 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512138 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 127 changed. pass 2: 8 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (26219 26222 26225) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 11:47:56 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 11:47:56 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-6.0.0/0050566/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-604 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-6.0.0/0050566/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-604 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 11:47:56 CEST 2017 Ended at Sun Oct 8 11:48:02 CEST 2017 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 11:48:02 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 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 0050566 $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 0050566 sysname Linux hostname tars-604 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1406379 mm^3 (det: 1.385193 ) Computing euler number orig.nofix lheno = -134, rheno = -78 orig.nofix lhholes = 68, rhholes = 40 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 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 11:49:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566 mri_aparc2aseg --s 0050566 --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 0050566 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-6.0.0/0050566/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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-6.0.0/0050566/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7826 vertices from left hemi Ripped 8221 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-6.0.0/0050566/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 = 936872 Used brute-force search on 203 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1.000000 1 k 2.000000 2 k 1497.000000 3 k 1.000000 4 k 16.000000 Fixing Parahip RH WM Found 7 clusters 0 k 1426.000000 1 k 1.000000 2 k 2.000000 3 k 26.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050566 --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 0050566 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-604 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1406379 mm^3 (det: 1.385193 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 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-6.0.0/0050566/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 11:58:21 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 26927 of (26927 26933 26939 26947 26954) to complete... Waiting for PID 26933 of (26927 26933 26939 26947 26954) to complete... Waiting for PID 26939 of (26927 26933 26939 26947 26954) to complete... Waiting for PID 26947 of (26927 26933 26939 26947 26954) to complete... Waiting for PID 26954 of (26927 26933 26939 26947 26954) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4332 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 373 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8282 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4162 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6124 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6004 mri_label2label: Done PIDs (26927 26933 26939 26947 26954) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 27007 of (27007 27013 27019 27024) to complete... Waiting for PID 27013 of (27007 27013 27019 27024) to complete... Waiting for PID 27019 of (27007 27013 27019 27024) to complete... Waiting for PID 27024 of (27007 27013 27019 27024) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4140 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 1108 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14697 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 304 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4485 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 577 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3999 mri_label2label: Done PIDs (27007 27013 27019 27024) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 27073 of (27073 27079 27085 27091 27097) to complete... Waiting for PID 27079 of (27073 27079 27085 27091 27097) to complete... Waiting for PID 27085 of (27073 27079 27085 27091 27097) to complete... Waiting for PID 27091 of (27073 27079 27085 27091 27097) to complete... Waiting for PID 27097 of (27073 27079 27085 27091 27097) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 1155 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5796 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 2403 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10517 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 418 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2436 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1336 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1262 mri_label2label: Done PIDs (27073 27079 27085 27091 27097) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 27150 of (27150 27156 27162 27168 27173) to complete... Waiting for PID 27156 of (27150 27156 27162 27168 27173) to complete... Waiting for PID 27162 of (27150 27156 27162 27168 27173) to complete... Waiting for PID 27168 of (27150 27156 27162 27168 27173) to complete... Waiting for PID 27173 of (27150 27156 27162 27168 27173) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1088 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2210 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1526 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2079 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2419 mri_label2label: Done PIDs (27150 27156 27162 27168 27173) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 27223 of (27223 27229 27235 27240) to complete... Waiting for PID 27229 of (27223 27229 27235 27240) to complete... Waiting for PID 27235 of (27223 27229 27235 27240) to complete... Waiting for PID 27240 of (27223 27229 27235 27240) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1580 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 467 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 158 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2070 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 167 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1318 mri_label2label: Done PIDs (27223 27229 27235 27240) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 27310 of (27310 27316 27322 27328 27332) to complete... Waiting for PID 27316 of (27310 27316 27322 27328 27332) to complete... Waiting for PID 27322 of (27310 27316 27322 27328 27332) to complete... Waiting for PID 27328 of (27310 27316 27322 27328 27332) to complete... Waiting for PID 27332 of (27310 27316 27322 27328 27332) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 779 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4184 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 1125 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4459 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 633 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 492 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 121292 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 457 mri_label2label: Done PIDs (27310 27316 27322 27328 27332) completed and logs appended. mris_label2annot --s 0050566 --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-6.0.0/0050566/label cmdline mris_label2annot --s 0050566 --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-604 machine x86_64 user ntraut subject 0050566 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-6.0.0/0050566/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 82973 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/lh.BA_exvivo.annot mris_label2annot --s 0050566 --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-6.0.0/0050566/label cmdline mris_label2annot --s 0050566 --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-604 machine x86_64 user ntraut subject 0050566 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-6.0.0/0050566/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 99059 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 255377 Total vertex volume 251169 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 1003 710 2771 2.571 0.917 0.143 0.030 11 1.2 BA1_exvivo 3721 2531 6306 2.380 0.555 0.098 0.017 22 2.7 BA2_exvivo 889 624 885 1.836 0.428 0.140 0.025 9 0.7 BA3a_exvivo 1869 1346 3601 1.979 0.833 0.112 0.021 18 1.6 BA3b_exvivo 1511 1030 3337 2.627 0.653 0.120 0.026 14 1.8 BA4a_exvivo 1023 722 1720 2.428 0.499 0.092 0.013 5 0.6 BA4p_exvivo 8900 6391 21275 2.748 0.725 0.121 0.024 86 8.8 BA6_exvivo 2217 1571 4959 2.462 0.726 0.124 0.027 30 2.5 BA44_exvivo 2785 1970 5812 2.406 0.611 0.128 0.030 31 3.3 BA45_exvivo 3273 2548 4507 1.718 0.596 0.158 0.042 45 6.3 V1_exvivo 7925 5642 13508 2.190 0.605 0.151 0.037 110 12.3 V2_exvivo 2081 1436 4258 2.503 0.700 0.112 0.023 19 1.8 MT_exvivo 533 359 1960 3.639 0.803 0.110 0.022 4 0.5 perirhinal_exvivo 589 476 2017 3.480 0.926 0.141 0.034 7 0.8 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 0050566 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 255377 Total vertex volume 251169 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 641 432 1929 2.800 0.970 0.168 0.037 11 1.0 BA1_exvivo 1517 1027 2757 2.422 0.503 0.089 0.014 9 0.8 BA2_exvivo 734 517 715 1.881 0.420 0.147 0.027 8 0.6 BA3a_exvivo 1229 914 1818 1.646 0.582 0.085 0.012 5 0.6 BA3b_exvivo 1382 971 3020 2.623 0.649 0.108 0.022 10 1.3 BA4a_exvivo 897 624 1445 2.387 0.489 0.097 0.015 5 0.6 BA4p_exvivo 4853 3526 12040 2.805 0.694 0.128 0.026 51 5.2 BA6_exvivo 1379 982 3181 2.441 0.736 0.136 0.029 24 1.8 BA44_exvivo 1049 746 2664 2.579 0.577 0.142 0.040 16 1.6 BA45_exvivo 3482 2701 4878 1.705 0.582 0.151 0.041 44 6.3 V1_exvivo 3943 2882 6963 2.200 0.658 0.165 0.044 63 7.5 V2_exvivo 558 388 1274 2.657 0.756 0.121 0.023 5 0.5 MT_exvivo 275 192 1160 3.779 0.698 0.093 0.014 1 0.2 perirhinal_exvivo 294 223 833 3.433 0.719 0.093 0.017 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 12:01:18 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 27461 of (27461 27467 27473 27478 27483) to complete... Waiting for PID 27467 of (27461 27467 27473 27478 27483) to complete... Waiting for PID 27473 of (27461 27467 27473 27478 27483) to complete... Waiting for PID 27478 of (27461 27467 27473 27478 27483) to complete... Waiting for PID 27483 of (27461 27467 27473 27478 27483) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4315 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 474 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7161 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4033 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4746 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 316 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6063 mri_label2label: Done PIDs (27461 27467 27473 27478 27483) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 27677 of (27677 27683 27689 27694) to complete... Waiting for PID 27683 of (27677 27683 27689 27694) to complete... Waiting for PID 27689 of (27677 27683 27689 27694) to complete... Waiting for PID 27694 of (27677 27683 27689 27694) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4613 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 663 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12919 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 564 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7476 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 650 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6005 mri_label2label: Done PIDs (27677 27683 27689 27694) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 27745 of (27745 27751 27757 27762 27767) to complete... Waiting for PID 27751 of (27745 27751 27757 27762 27767) to complete... Waiting for PID 27757 of (27745 27751 27757 27762 27767) to complete... Waiting for PID 27762 of (27745 27751 27757 27762 27767) to complete... Waiting for PID 27767 of (27745 27751 27757 27762 27767) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 1772 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6499 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 2802 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10818 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2224 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1125 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 827 mri_label2label: Done PIDs (27745 27751 27757 27762 27767) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 27823 of (27823 27829 27835 27840 27847) to complete... Waiting for PID 27829 of (27823 27829 27835 27840 27847) to complete... Waiting for PID 27835 of (27823 27829 27835 27840 27847) to complete... Waiting for PID 27840 of (27823 27829 27835 27840 27847) to complete... Waiting for PID 27847 of (27823 27829 27835 27840 27847) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 973 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2827 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1728 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2263 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1476 mri_label2label: Done PIDs (27823 27829 27835 27840 27847) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 27896 of (27896 27902 27908 27913) to complete... Waiting for PID 27902 of (27896 27902 27908 27913) to complete... Waiting for PID 27908 of (27896 27902 27908 27913) to complete... Waiting for PID 27913 of (27896 27902 27908 27913) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1501 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7333 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 151 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1163 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 167 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1345 mri_label2label: Done PIDs (27896 27902 27908 27913) 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 0050566 --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 0050566 --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 0050566 --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 0050566 --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 0050566 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 27959 of (27959 27965 27971 27975 27982) to complete... Waiting for PID 27965 of (27959 27965 27971 27975 27982) to complete... Waiting for PID 27971 of (27959 27965 27971 27975 27982) to complete... Waiting for PID 27975 of (27959 27965 27971 27975 27982) to complete... Waiting for PID 27982 of (27959 27965 27971 27975 27982) 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 1231 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4463 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 1291 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4728 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 312 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 737 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 0050566 --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 = 0050566 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-6.0.0/0050566/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 125464 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 306 mri_label2label: Done PIDs (27959 27965 27971 27975 27982) completed and logs appended. mris_label2annot --s 0050566 --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-6.0.0/0050566/label cmdline mris_label2annot --s 0050566 --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-604 machine x86_64 user ntraut subject 0050566 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-6.0.0/0050566/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 86226 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/label/rh.BA_exvivo.annot mris_label2annot --s 0050566 --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-6.0.0/0050566/label cmdline mris_label2annot --s 0050566 --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-604 machine x86_64 user ntraut subject 0050566 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-6.0.0/0050566/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 103091 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/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 0050566 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 268912 Total vertex volume 264656 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 965 633 2047 2.262 0.867 0.175 0.050 30 2.5 BA1_exvivo 3281 2146 4879 2.259 0.615 0.089 0.016 16 2.0 BA2_exvivo 974 603 814 1.680 0.472 0.115 0.017 8 0.6 BA3a_exvivo 1663 1113 2751 1.879 0.847 0.086 0.020 12 1.3 BA3b_exvivo 1385 901 2787 2.588 0.597 0.108 0.027 10 1.7 BA4a_exvivo 923 659 1386 2.189 0.604 0.080 0.014 3 0.6 BA4p_exvivo 7441 5119 18165 2.833 0.772 0.118 0.026 84 8.0 BA6_exvivo 3468 2440 7348 2.560 0.748 0.117 0.023 36 3.5 BA44_exvivo 3839 2694 9273 2.613 0.787 0.118 0.022 39 3.5 BA45_exvivo 4286 3003 5822 1.782 0.577 0.145 0.039 56 7.1 V1_exvivo 8202 5799 13451 2.132 0.683 0.144 0.035 107 12.1 V2_exvivo 1845 1288 3528 2.549 0.616 0.137 0.030 23 2.2 MT_exvivo 583 385 2258 3.622 0.882 0.101 0.022 4 0.5 perirhinal_exvivo 383 250 1064 3.316 0.845 0.110 0.023 3 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 0050566 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050566/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 268912 Total vertex volume 264656 (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) = 1406379 mm^3 (det: 1.385193 ) lhCtxGM: 250308.108 250379.000 diff= -70.9 pctdiff=-0.028 rhCtxGM: 262877.757 263225.000 diff= -347.2 pctdiff=-0.132 lhCtxWM: 211302.320 211100.000 diff= 202.3 pctdiff= 0.096 rhCtxWM: 214124.692 214747.000 diff= -622.3 pctdiff=-0.291 SubCortGMVol 58322.000 SupraTentVol 1011354.877 (1009543.000) diff=1811.877 pctdiff=0.179 SupraTentVolNotVent 999594.877 (997783.000) diff=1811.877 pctdiff=0.181 BrainSegVol 1172110.000 (1169539.000) diff=2571.000 pctdiff=0.219 BrainSegVolNotVent 1156881.000 (1155925.877) diff=955.123 pctdiff=0.083 BrainSegVolNotVent 1156881.000 CerebellumVol 158981.000 VentChorVol 11760.000 3rd4th5thCSF 3469.000 CSFVol 898.000, OptChiasmVol 117.000 MaskVol 1524839.000 629 433 1277 2.143 0.745 0.166 0.046 14 1.3 BA1_exvivo 1860 1177 2891 2.210 0.604 0.073 0.012 7 1.0 BA2_exvivo 873 538 626 1.605 0.349 0.115 0.016 7 0.5 BA3a_exvivo 1314 883 1686 1.614 0.605 0.070 0.013 7 0.6 BA3b_exvivo 937 595 1814 2.662 0.562 0.123 0.038 8 1.5 BA4a_exvivo 779 549 1160 2.309 0.609 0.071 0.012 2 0.4 BA4p_exvivo 4751 3258 11662 2.832 0.772 0.123 0.027 62 5.6 BA6_exvivo 923 683 2716 2.826 0.776 0.163 0.034 18 1.4 BA44_exvivo 1076 770 3412 2.857 0.840 0.139 0.030 17 1.4 BA45_exvivo 4067 2848 5226 1.739 0.519 0.144 0.037 52 6.6 V1_exvivo 4314 3142 7546 2.148 0.768 0.154 0.039 61 7.3 V2_exvivo 264 183 729 2.845 0.623 0.152 0.028 5 0.3 MT_exvivo 337 227 1261 3.581 0.860 0.076 0.016 1 0.2 perirhinal_exvivo 249 170 715 3.320 0.783 0.110 0.020 1 0.2 entorhinal_exvivo Started at Sun Oct 8 01:37:07 CEST 2017 Ended at Sun Oct 8 12:04:18 CEST 2017 #@#%# recon-all-run-time-hours 10.453 recon-all -s 0050566 finished without error at Sun Oct 8 12:04:18 CEST 2017